Re: [Bioc-devel] BSgenome changes

2020-08-20 Thread Hervé Pagès 

Kasper,

The tradition so far has been to package all UCSC human genomes since 
hg17. We could also start producing BSgenome packages for other non-UCSC 
Human assemblies. We just need to draw a line somewhere. If there is a 
need for it we can make BSgenome.Hsapiens.NCBI.GRCh37.p13 available, as 
I said earlier. Is this what you are asking for?


H.

On 8/20/20 03:23, Kasper Daniel Hansen wrote:
Well, the presence of two mitochondrial genomes is to fix a mistake by 
UCSC. I can appreciate the importance of representing this mistake when 
you build off UCSC. But it strikes me as not actually representing the 
h37 version of the genome, and it seems to me that we want such a 
representation in the project - not everything comes through UCSC. But 
perhaps I have not given this sufficient thought, this is just my 
immediate reaction.


On Tue, Aug 18, 2020 at 8:18 PM Leonard Goldstein 
mailto:goldstein.leon...@gene.com>> wrote:


Thanks for the explanation Hervé.

Best wishes

Leonard


On Tue, Aug 18, 2020 at 10:06 AM Hervé Pagès mailto:hpa...@fredhutch.org>> wrote:

On 8/18/20 01:40, Kasper Daniel Hansen wrote:
 > In light of this, could we get a version of GRCh37 with only
a single
 > mitochondrial genome?

You mean a BSgenome.Hsapiens.NCBI.GRCh37.p13 package? So it would
contain the same sequences as BSgenome.Hsapiens.UCSC.hg19 but
without
the hg19:chrM sequence?

Certainly doable but note that by using
BSgenome.Hsapiens.UCSC.hg38 you
stay away from this mess. I'm not sure that adding yet another
BSgenome
package would make the situation less confusing.

 >
 > On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès
mailto:hpa...@fredhutch.org>
 > <mailto:hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>>>
wrote:
 >
 >     Hi Felix,
 >
 >     On 8/13/20 21:43, Felix Ernst wrote:
 >      > Hi Leonard, Hi Herve,
 >      >
 >      > I followed your conversation, since I have noticed the
same
 >     problem. Thanks, Herve, for the explanation of the recent
changes on
 >     hg19.
 >      >
 >      > The GRCh37.P13 report states in its last line:
 >      >
 >      > MT    assembled-molecule      MT      Mitochondrion 
  J01415.2

 >          =       NC_012920.1     non-nuclear     16569   chrM
 >      >
 >      > Since the last name is called "UCSC-style-name",
wouldn't that
 >     mean that chrM has to be renamed to MT and not chrMT?
 >
 >     This is a mistake in the sequence report for GRCh37.p13.
GRCh37.p13:MT
 >     is the same as hg19:chrMT, not hg19:chrM.
 >
 >     hg19:chrM and hg19:chrMT are **not** the same sequences.
The former is
 >     NC_001807 and has length 16571 and the latter is
NC_012920.1 and has
 >     length 16569.
 >
 >     Yes, seqlevelsStyle() is sorting out all this mess for
you ;-)
 >
 >     Cheers,
 >     H.
 >
 >      >
 >      > Thanks again for the explanation.
 >      >
 >      > Cheers,
 >      > Felix
 >      >
 >      > -Ursprüngliche Nachricht-
 >      > Von: Bioc-devel mailto:bioc-devel-boun...@r-project.org>
 >     <mailto:bioc-devel-boun...@r-project.org
<mailto:bioc-devel-boun...@r-project.org>>> Im Auftrag von Hervé
Pagès
 >      > Gesendet: Freitag, 14. August 2020 01:08
 >      > An: Leonard Goldstein mailto:goldstein.leon...@gene.com>
 >     <mailto:goldstein.leon...@gene.com
<mailto:goldstein.leon...@gene.com>>>; bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
         >     <mailto:bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>>
 >      > Cc: charlotte.sone...@fmi.ch
<mailto:charlotte.sone...@fmi.ch>
<mailto:charlotte.sone...@fmi.ch <mailto:charlotte.sone...@fmi.ch>>
 >      > Betreff: Re: [Bioc-devel] BSgenome changes
 >      >
 >      > Hi Leonard,
 >      >
 >      > On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
 >      >> Dear Bioc team,
 >      >>
 >      >> I'm following up on this recent GitHub issue
 >      >>

Re: [Bioc-devel] BSgenome changes

2020-08-20 Thread Kasper Daniel Hansen 
Well, the presence of two mitochondrial genomes is to fix a mistake by
UCSC. I can appreciate the importance of representing this mistake when you
build off UCSC. But it strikes me as not actually representing the h37
version of the genome, and it seems to me that we want such a
representation in the project - not everything comes through UCSC. But
perhaps I have not given this sufficient thought, this is just my immediate
reaction.

On Tue, Aug 18, 2020 at 8:18 PM Leonard Goldstein <
goldstein.leon...@gene.com> wrote:

> Thanks for the explanation Hervé.
>
> Best wishes
>
> Leonard
>
>
> On Tue, Aug 18, 2020 at 10:06 AM Hervé Pagès  wrote:
>
>> On 8/18/20 01:40, Kasper Daniel Hansen wrote:
>> > In light of this, could we get a version of GRCh37 with only a single
>> > mitochondrial genome?
>>
>> You mean a BSgenome.Hsapiens.NCBI.GRCh37.p13 package? So it would
>> contain the same sequences as BSgenome.Hsapiens.UCSC.hg19 but without
>> the hg19:chrM sequence?
>>
>> Certainly doable but note that by using BSgenome.Hsapiens.UCSC.hg38 you
>> stay away from this mess. I'm not sure that adding yet another BSgenome
>> package would make the situation less confusing.
>>
>> >
>> > On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès > > <mailto:hpa...@fredhutch.org>> wrote:
>> >
>> > Hi Felix,
>> >
>> > On 8/13/20 21:43, Felix Ernst wrote:
>> >  > Hi Leonard, Hi Herve,
>> >  >
>> >  > I followed your conversation, since I have noticed the same
>> > problem. Thanks, Herve, for the explanation of the recent changes on
>> > hg19.
>> >  >
>> >  > The GRCh37.P13 report states in its last line:
>> >  >
>> >  > MTassembled-molecule  MT  Mitochondrion   J01415.2
>> >  =   NC_012920.1 non-nuclear 16569   chrM
>> >  >
>> >  > Since the last name is called "UCSC-style-name", wouldn't that
>> > mean that chrM has to be renamed to MT and not chrMT?
>> >
>> > This is a mistake in the sequence report for GRCh37.p13.
>> GRCh37.p13:MT
>> > is the same as hg19:chrMT, not hg19:chrM.
>> >
>> > hg19:chrM and hg19:chrMT are **not** the same sequences. The former
>> is
>> > NC_001807 and has length 16571 and the latter is NC_012920.1 and has
>> > length 16569.
>> >
>> > Yes, seqlevelsStyle() is sorting out all this mess for you ;-)
>> >
>> > Cheers,
>> > H.
>> >
>> >  >
>> >  > Thanks again for the explanation.
>> >  >
>> >  > Cheers,
>> >  > Felix
>> >  >
>> >  > -Ursprüngliche Nachricht-
>> >  > Von: Bioc-devel > > <mailto:bioc-devel-boun...@r-project.org>> Im Auftrag von Hervé
>> Pagès
>> >  > Gesendet: Freitag, 14. August 2020 01:08
>> >  > An: Leonard Goldstein > > <mailto:goldstein.leon...@gene.com>>; bioc-devel@r-project.org
>> > <mailto:bioc-devel@r-project.org>
>> >  > Cc: charlotte.sone...@fmi.ch <mailto:charlotte.sone...@fmi.ch>
>> >  > Betreff: Re: [Bioc-devel] BSgenome changes
>> >  >
>> >  > Hi Leonard,
>> >  >
>> >  > On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
>> >  >> Dear Bioc team,
>> >  >>
>> >  >> I'm following up on this recent GitHub issue
>> >  >>
>> > <
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
>> >  >>
>> >
>>  
>> _SGSeq_issues_5=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE=
>> >  >. Please see the issue for more details and code examples.
>> >  >>
>> >  >> It looks like changes in Bioc devel result in two copies of the
>> >  >> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one
>> > named
>> >  >> chrM like in previous package versions (length 16571) and one
>> named
>> >  >> chrMT (length 16569).
>> >  >>
>> >  >> When using seqlevelsStyle() to change chromosome names from
>> UCSC to
>> >  >> NCBI format, this results

Re: [Bioc-devel] BSgenome changes

2020-08-18 Thread Leonard Goldstein via Bioc-devel 
Thanks for the explanation Hervé.

Best wishes

Leonard


On Tue, Aug 18, 2020 at 10:06 AM Hervé Pagès  wrote:

> On 8/18/20 01:40, Kasper Daniel Hansen wrote:
> > In light of this, could we get a version of GRCh37 with only a single
> > mitochondrial genome?
>
> You mean a BSgenome.Hsapiens.NCBI.GRCh37.p13 package? So it would
> contain the same sequences as BSgenome.Hsapiens.UCSC.hg19 but without
> the hg19:chrM sequence?
>
> Certainly doable but note that by using BSgenome.Hsapiens.UCSC.hg38 you
> stay away from this mess. I'm not sure that adding yet another BSgenome
> package would make the situation less confusing.
>
> >
> > On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès  > <mailto:hpa...@fredhutch.org>> wrote:
> >
> > Hi Felix,
> >
> > On 8/13/20 21:43, Felix Ernst wrote:
> >  > Hi Leonard, Hi Herve,
> >  >
> >  > I followed your conversation, since I have noticed the same
> > problem. Thanks, Herve, for the explanation of the recent changes on
> > hg19.
> >  >
> >  > The GRCh37.P13 report states in its last line:
> >  >
> >  > MTassembled-molecule  MT  Mitochondrion   J01415.2
> >  =   NC_012920.1 non-nuclear 16569   chrM
> >  >
> >  > Since the last name is called "UCSC-style-name", wouldn't that
> > mean that chrM has to be renamed to MT and not chrMT?
> >
> > This is a mistake in the sequence report for GRCh37.p13.
> GRCh37.p13:MT
> > is the same as hg19:chrMT, not hg19:chrM.
> >
> > hg19:chrM and hg19:chrMT are **not** the same sequences. The former
> is
> > NC_001807 and has length 16571 and the latter is NC_012920.1 and has
> > length 16569.
> >
> > Yes, seqlevelsStyle() is sorting out all this mess for you ;-)
> >
> > Cheers,
> > H.
> >
> >  >
> >  > Thanks again for the explanation.
> >  >
> >  > Cheers,
> >  > Felix
> >  >
> >  > -Ursprüngliche Nachricht-
> >  > Von: Bioc-devel  > <mailto:bioc-devel-boun...@r-project.org>> Im Auftrag von Hervé
> Pagès
> >  > Gesendet: Freitag, 14. August 2020 01:08
> >  > An: Leonard Goldstein  > <mailto:goldstein.leon...@gene.com>>; bioc-devel@r-project.org
> > <mailto:bioc-devel@r-project.org>
> >  > Cc: charlotte.sone...@fmi.ch <mailto:charlotte.sone...@fmi.ch>
> >  > Betreff: Re: [Bioc-devel] BSgenome changes
> >  >
> >  > Hi Leonard,
> >  >
> >  > On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
> >  >> Dear Bioc team,
> >  >>
> >  >> I'm following up on this recent GitHub issue
> >  >>
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
> >  >>
> >
>  
> _SGSeq_issues_5=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE=
> >  >. Please see the issue for more details and code examples.
> >  >>
> >  >> It looks like changes in Bioc devel result in two copies of the
> >  >> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one
> > named
> >  >> chrM like in previous package versions (length 16571) and one
> named
> >  >> chrMT (length 16569).
> >  >>
> >  >> When using seqlevelsStyle() to change chromosome names from UCSC
> to
> >  >> NCBI format, this results in new behavior -- in the past chrM was
> >  >> simply renamed MT, now the different sequence chrMT is used. Is
> > this intended?
> >  >
> >  > Absolutely intended.
> >  >
> >  > There is a long story behind the unfortunate fate of the
> > mitochondrial chromosome in hg19. I'll try to keep it short.
> >  >
> >  > When the UCSC folks released the hg19 browser more than 10 years
> > ago, they based it on assembly GRCh37:
> >  >
> >  >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.13=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=jWtgKVQGC-SQp6i4prhKBiD5cBh2kEc8R1gL2uPlzy0=
> >  >
> >  > See sequence re

Re: [Bioc-devel] BSgenome changes

2020-08-18 Thread Hervé Pagès 

On 8/18/20 01:40, Kasper Daniel Hansen wrote:
In light of this, could we get a version of GRCh37 with only a single 
mitochondrial genome?


You mean a BSgenome.Hsapiens.NCBI.GRCh37.p13 package? So it would 
contain the same sequences as BSgenome.Hsapiens.UCSC.hg19 but without 
the hg19:chrM sequence?


Certainly doable but note that by using BSgenome.Hsapiens.UCSC.hg38 you 
stay away from this mess. I'm not sure that adding yet another BSgenome 
package would make the situation less confusing.




On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès <mailto:hpa...@fredhutch.org>> wrote:


Hi Felix,

On 8/13/20 21:43, Felix Ernst wrote:
 > Hi Leonard, Hi Herve,
 >
 > I followed your conversation, since I have noticed the same
problem. Thanks, Herve, for the explanation of the recent changes on
hg19.
 >
 > The GRCh37.P13 report states in its last line:
 >
 > MT    assembled-molecule      MT      Mitochondrion   J01415.2   
     =       NC_012920.1     non-nuclear     16569   chrM

 >
 > Since the last name is called "UCSC-style-name", wouldn't that
mean that chrM has to be renamed to MT and not chrMT?

This is a mistake in the sequence report for GRCh37.p13. GRCh37.p13:MT
is the same as hg19:chrMT, not hg19:chrM.

hg19:chrM and hg19:chrMT are **not** the same sequences. The former is
NC_001807 and has length 16571 and the latter is NC_012920.1 and has
length 16569.

Yes, seqlevelsStyle() is sorting out all this mess for you ;-)

Cheers,
H.

 >
 > Thanks again for the explanation.
 >
 > Cheers,
 > Felix
 >
 > -Ursprüngliche Nachricht-
 > Von: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> Im Auftrag von Hervé Pagès
 > Gesendet: Freitag, 14. August 2020 01:08
 > An: Leonard Goldstein mailto:goldstein.leon...@gene.com>>; bioc-devel@r-project.org
<mailto:bioc-devel@r-project.org>
     > Cc: charlotte.sone...@fmi.ch <mailto:charlotte.sone...@fmi.ch>
 > Betreff: Re: [Bioc-devel] BSgenome changes
 >
 > Hi Leonard,
 >
 > On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
 >> Dear Bioc team,
 >>
 >> I'm following up on this recent GitHub issue
 >>
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
 >>

_SGSeq_issues_5=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE=
 >. Please see the issue for more details and code examples.
 >>
 >> It looks like changes in Bioc devel result in two copies of the
 >> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one
named
 >> chrM like in previous package versions (length 16571) and one named
 >> chrMT (length 16569).
 >>
 >> When using seqlevelsStyle() to change chromosome names from UCSC to
 >> NCBI format, this results in new behavior -- in the past chrM was
 >> simply renamed MT, now the different sequence chrMT is used. Is
this intended?
 >
 > Absolutely intended.
 >
 > There is a long story behind the unfortunate fate of the
mitochondrial chromosome in hg19. I'll try to keep it short.
 >
 > When the UCSC folks released the hg19 browser more than 10 years
ago, they based it on assembly GRCh37:
 >
 >

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.13=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=jWtgKVQGC-SQp6i4prhKBiD5cBh2kEc8R1gL2uPlzy0=
 >
 > See sequence report for GRCh37:
 >
 >
 >

https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F01405.13-5FGRCh37_GCF-5F01405.13-5FGRCh37-5Fassembly-5Freport.txt=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=2mzBk6ksCERabHcDIy7tR6p1aQvFGkLM8lZNrsWrA18=
 >
 > For some mysterious reason GRCh37 didn't include the
mitochondrial chromosome so the UCSC folks decided to use
mitochondrial sequence
 > NC_001807 and called it chrM.
 >
 > However, UCSC has recently decided to base hg19 on GRCh37.p13
instead of GRCh37. A rather surprising move after many years of hg19
being based on the latter.
 >
 >

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.25_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=gxOOdwtmHjZfz-

Re: [Bioc-devel] BSgenome changes

2020-08-18 Thread Kasper Daniel Hansen 
In light of this, could we get a version of GRCh37 with only a single
mitochondrial genome?

On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès  wrote:

> Hi Felix,
>
> On 8/13/20 21:43, Felix Ernst wrote:
> > Hi Leonard, Hi Herve,
> >
> > I followed your conversation, since I have noticed the same problem.
> Thanks, Herve, for the explanation of the recent changes on hg19.
> >
> > The GRCh37.P13 report states in its last line:
> >
> > MTassembled-molecule  MT  Mitochondrion   J01415.2=
>  NC_012920.1 non-nuclear 16569   chrM
> >
> > Since the last name is called "UCSC-style-name", wouldn't that mean that
> chrM has to be renamed to MT and not chrMT?
>
> This is a mistake in the sequence report for GRCh37.p13. GRCh37.p13:MT
> is the same as hg19:chrMT, not hg19:chrM.
>
> hg19:chrM and hg19:chrMT are **not** the same sequences. The former is
> NC_001807 and has length 16571 and the latter is NC_012920.1 and has
> length 16569.
>
> Yes, seqlevelsStyle() is sorting out all this mess for you ;-)
>
> Cheers,
> H.
>
> >
> > Thanks again for the explanation.
> >
> > Cheers,
> > Felix
> >
> > -Ursprüngliche Nachricht-
> > Von: Bioc-devel  Im Auftrag von Hervé
> Pagès
> > Gesendet: Freitag, 14. August 2020 01:08
> > An: Leonard Goldstein ;
> bioc-devel@r-project.org
> > Cc: charlotte.sone...@fmi.ch
> > Betreff: Re: [Bioc-devel] BSgenome changes
> >
> > Hi Leonard,
> >
> > On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
> >> Dear Bioc team,
> >>
> >> I'm following up on this recent GitHub issue
> >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
> >>
> _SGSeq_issues_5=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE=
> >. Please see the issue for more details and code examples.
> >>
> >> It looks like changes in Bioc devel result in two copies of the
> >> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named
> >> chrM like in previous package versions (length 16571) and one named
> >> chrMT (length 16569).
> >>
> >> When using seqlevelsStyle() to change chromosome names from UCSC to
> >> NCBI format, this results in new behavior -- in the past chrM was
> >> simply renamed MT, now the different sequence chrMT is used. Is this
> intended?
> >
> > Absolutely intended.
> >
> > There is a long story behind the unfortunate fate of the mitochondrial
> chromosome in hg19. I'll try to keep it short.
> >
> > When the UCSC folks released the hg19 browser more than 10 years ago,
> they based it on assembly GRCh37:
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.13=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=jWtgKVQGC-SQp6i4prhKBiD5cBh2kEc8R1gL2uPlzy0=
> >
> > See sequence report for GRCh37:
> >
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F01405.13-5FGRCh37_GCF-5F01405.13-5FGRCh37-5Fassembly-5Freport.txt=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=2mzBk6ksCERabHcDIy7tR6p1aQvFGkLM8lZNrsWrA18=
> >
> > For some mysterious reason GRCh37 didn't include the mitochondrial
> chromosome so the UCSC folks decided to use mitochondrial sequence
> > NC_001807 and called it chrM.
> >
> > However, UCSC has recently decided to base hg19 on GRCh37.p13 instead of
> GRCh37. A rather surprising move after many years of hg19 being based on
> the latter.
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.25_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=gxOOdwtmHjZfz-EAFblY0cm-7upZ9useI3sEgDD87o8=
> >
> > See sequence report for GRCh37.p13:
> >
> >
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F01405.25-5FGRCh37.p13_GCF-5F01405.25-5FGRCh37.p13-5Fassembly-5Freport.txt=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=epUg7bSfwCEF_WUOPlT5hPmLXHY7V51Mau09UaQNB5o=
> >
> > Note that GRCh37.p13 does include the mitochondrial chromosome. It's
> called MT in t

Re: [Bioc-devel] BSgenome changes

2020-08-14 Thread Hervé Pagès 

Hi Felix,

On 8/13/20 21:43, Felix Ernst wrote:

Hi Leonard, Hi Herve,

I followed your conversation, since I have noticed the same problem. Thanks, 
Herve, for the explanation of the recent changes on hg19.

The GRCh37.P13 report states in its last line:

MT  assembled-molecule  MT  Mitochondrion   J01415.2=   
NC_012920.1 non-nuclear 16569   chrM

Since the last name is called "UCSC-style-name", wouldn't that mean that chrM 
has to be renamed to MT and not chrMT?


This is a mistake in the sequence report for GRCh37.p13. GRCh37.p13:MT 
is the same as hg19:chrMT, not hg19:chrM.


hg19:chrM and hg19:chrMT are **not** the same sequences. The former is 
NC_001807 and has length 16571 and the latter is NC_012920.1 and has 
length 16569.


Yes, seqlevelsStyle() is sorting out all this mess for you ;-)

Cheers,
H.



Thanks again for the explanation.

Cheers,
Felix

-Ursprüngliche Nachricht-
Von: Bioc-devel  Im Auftrag von Hervé Pagès
Gesendet: Freitag, 14. August 2020 01:08
An: Leonard Goldstein ; bioc-devel@r-project.org
Cc: charlotte.sone...@fmi.ch
Betreff: Re: [Bioc-devel] BSgenome changes

Hi Leonard,

On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:

Dear Bioc team,

I'm following up on this recent GitHub issue
<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
_SGSeq_issues_5=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE=
 >. Please see the issue for more details and code examples.

It looks like changes in Bioc devel result in two copies of the
mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named
chrM like in previous package versions (length 16571) and one named
chrMT (length 16569).

When using seqlevelsStyle() to change chromosome names from UCSC to
NCBI format, this results in new behavior -- in the past chrM was
simply renamed MT, now the different sequence chrMT is used. Is this intended?


Absolutely intended.

There is a long story behind the unfortunate fate of the mitochondrial 
chromosome in hg19. I'll try to keep it short.

When the UCSC folks released the hg19 browser more than 10 years ago, they 
based it on assembly GRCh37:


https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.13=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=jWtgKVQGC-SQp6i4prhKBiD5cBh2kEc8R1gL2uPlzy0=

See sequence report for GRCh37:

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F01405.13-5FGRCh37_GCF-5F01405.13-5FGRCh37-5Fassembly-5Freport.txt=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=2mzBk6ksCERabHcDIy7tR6p1aQvFGkLM8lZNrsWrA18=


For some mysterious reason GRCh37 didn't include the mitochondrial chromosome 
so the UCSC folks decided to use mitochondrial sequence
NC_001807 and called it chrM.

However, UCSC has recently decided to base hg19 on GRCh37.p13 instead of 
GRCh37. A rather surprising move after many years of hg19 being based on the 
latter.


https://urldefense.proofpoint.com/v2/url?u=https-3A__www.ncbi.nlm.nih.gov_assembly_GCF-5F01405.25_=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=gxOOdwtmHjZfz-EAFblY0cm-7upZ9useI3sEgDD87o8=

See sequence report for GRCh37.p13:

  
https://urldefense.proofpoint.com/v2/url?u=https-3A__ftp.ncbi.nlm.nih.gov_genomes_all_GCF_000_001_405_GCF-5F01405.25-5FGRCh37.p13_GCF-5F01405.25-5FGRCh37.p13-5Fassembly-5Freport.txt=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558=epUg7bSfwCEF_WUOPlT5hPmLXHY7V51Mau09UaQNB5o=


Note that GRCh37.p13 does include the mitochondrial chromosome. It's called MT 
in the official sequence report above and chrMT in hg19.

At the same time the UCSC folks decided to keep chrM so now hg19 contains 2 
mitochondrial sequences: chrM and chrMT. Previously it has only one: chrM.

So what you see in BioC devel in BSgenome.Hsapiens.UCSC.hg19 and with
seqlevelsStyle(genome) is only reflecting this. In particular
seqlevelsStyle(genome) <- "NCBI" now does the following:

- Rename chrMT -> MT.

- chrM does NOT get renamed. There is no point in renaming this sequence 
because it has no equivalent in GRCh37.p13.

Hope this helps,

H.



Leonard

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mail
man_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeA
vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYv
fbojaqTJZVg=IczvesjTwEk

Re: [Bioc-devel] BSgenome changes

2020-08-13 Thread Felix Ernst 
Hi Leonard, Hi Herve,

I followed your conversation, since I have noticed the same problem. Thanks, 
Herve, for the explanation of the recent changes on hg19.

The GRCh37.P13 report states in its last line:

MT  assembled-molecule  MT  Mitochondrion   J01415.2=   
NC_012920.1 non-nuclear 16569   chrM

Since the last name is called "UCSC-style-name", wouldn't that mean that chrM 
has to be renamed to MT and not chrMT?

Thanks again for the explanation.

Cheers,
Felix

-Ursprüngliche Nachricht-
Von: Bioc-devel  Im Auftrag von Hervé Pagès
Gesendet: Freitag, 14. August 2020 01:08
An: Leonard Goldstein ; bioc-devel@r-project.org
Cc: charlotte.sone...@fmi.ch
Betreff: Re: [Bioc-devel] BSgenome changes

Hi Leonard,

On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:
> Dear Bioc team,
> 
> I'm following up on this recent GitHub issue 
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_ldg21
> _SGSeq_issues_5=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE=
>  >. Please see the issue for more details and code examples.
> 
> It looks like changes in Bioc devel result in two copies of the 
> mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named 
> chrM like in previous package versions (length 16571) and one named 
> chrMT (length 16569).
> 
> When using seqlevelsStyle() to change chromosome names from UCSC to 
> NCBI format, this results in new behavior -- in the past chrM was 
> simply renamed MT, now the different sequence chrMT is used. Is this intended?

Absolutely intended.

There is a long story behind the unfortunate fate of the mitochondrial 
chromosome in hg19. I'll try to keep it short.

When the UCSC folks released the hg19 browser more than 10 years ago, they 
based it on assembly GRCh37:

   https://www.ncbi.nlm.nih.gov/assembly/GCF_01405.13

See sequence report for GRCh37:

 
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_01405.13_GRCh37/GCF_01405.13_GRCh37_assembly_report.txt

For some mysterious reason GRCh37 didn't include the mitochondrial chromosome 
so the UCSC folks decided to use mitochondrial sequence
NC_001807 and called it chrM.

However, UCSC has recently decided to base hg19 on GRCh37.p13 instead of 
GRCh37. A rather surprising move after many years of hg19 being based on the 
latter.

   https://www.ncbi.nlm.nih.gov/assembly/GCF_01405.25/

See sequence report for GRCh37.p13:

 
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_01405.25_GRCh37.p13/GCF_01405.25_GRCh37.p13_assembly_report.txt

Note that GRCh37.p13 does include the mitochondrial chromosome. It's called MT 
in the official sequence report above and chrMT in hg19.

At the same time the UCSC folks decided to keep chrM so now hg19 contains 2 
mitochondrial sequences: chrM and chrMT. Previously it has only one: chrM.

So what you see in BioC devel in BSgenome.Hsapiens.UCSC.hg19 and with
seqlevelsStyle(genome) is only reflecting this. In particular
seqlevelsStyle(genome) <- "NCBI" now does the following:

   - Rename chrMT -> MT.

   - chrM does NOT get renamed. There is no point in renaming this sequence 
because it has no equivalent in GRCh37.p13.

Hope this helps,

H.

> 
> Leonard
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mail
> man_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeA
> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYv
> fbojaqTJZVg=IczvesjTwEkPQVlFX5wKSJLUHyjNHE0sk71a-kMAVEI=
> 

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] BSgenome changes

2020-08-13 Thread Hervé Pagès 

Hi Leonard,

On 8/12/20 15:22, Leonard Goldstein via Bioc-devel wrote:

Dear Bioc team,

I'm following up on this recent GitHub issue
. Please see the issue for more
details and code examples.

It looks like changes in Bioc devel result in two copies of the
mitochondrial chromosome for BSgenome.Hsapiens.UCSC.hg19 -- one named chrM
like in previous package versions (length 16571) and one named chrMT
(length 16569).

When using seqlevelsStyle() to change chromosome names from UCSC to NCBI
format, this results in new behavior -- in the past chrM was simply renamed
MT, now the different sequence chrMT is used. Is this intended?


Absolutely intended.

There is a long story behind the unfortunate fate of the mitochondrial 
chromosome in hg19. I'll try to keep it short.


When the UCSC folks released the hg19 browser more than 10 years ago, 
they based it on assembly GRCh37:


  https://www.ncbi.nlm.nih.gov/assembly/GCF_01405.13

See sequence report for GRCh37:


https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_01405.13_GRCh37/GCF_01405.13_GRCh37_assembly_report.txt

For some mysterious reason GRCh37 didn't include the mitochondrial 
chromosome so the UCSC folks decided to use mitochondrial sequence 
NC_001807 and called it chrM.


However, UCSC has recently decided to base hg19 on GRCh37.p13 instead of 
GRCh37. A rather surprising move after many years of hg19 being based on 
the latter.


  https://www.ncbi.nlm.nih.gov/assembly/GCF_01405.25/

See sequence report for GRCh37.p13:


https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_01405.25_GRCh37.p13/GCF_01405.25_GRCh37.p13_assembly_report.txt

Note that GRCh37.p13 does include the mitochondrial chromosome. It's 
called MT in the official sequence report above and chrMT in hg19.


At the same time the UCSC folks decided to keep chrM so now hg19 
contains 2 mitochondrial sequences: chrM and chrMT. Previously it has 
only one: chrM.


So what you see in BioC devel in BSgenome.Hsapiens.UCSC.hg19 and with
seqlevelsStyle(genome) is only reflecting this. In particular 
seqlevelsStyle(genome) <- "NCBI" now does the following:


  - Rename chrMT -> MT.

  - chrM does NOT get renamed. There is no point in renaming this 
sequence because it has no equivalent in GRCh37.p13.


Hope this helps,

H.



Leonard

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel=DwICAg=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg=IczvesjTwEkPQVlFX5wKSJLUHyjNHE0sk71a-kMAVEI=



--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel