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 <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 <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 <goldstein.leon...@gene.com <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&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYvfbojaqTJZVg&s=Tfk-tDM99P63dnsvMydG2phv5WQPVbJzPk0hzi-_1SE&e= >. 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-5F000001405.13&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=jWtgKVQGC-SQp6i4prhKBiD5cBh2kEc8R1gL2uPlzy0&e= > > 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-5F000001405.13-5FGRCh37_GCF-5F000001405.13-5FGRCh37-5Fassembly-5Freport.txt&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=2mzBk6ksCERabHcDIy7tR6p1aQvFGkLM8lZNrsWrA18&e= > > 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-5F000001405.25_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=gxOOdwtmHjZfz-EAFblY0cm-7upZ9useI3sEgDD87o8&e= > > 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-5F000001405.25-5FGRCh37.p13_GCF-5F000001405.25-5FGRCh37.p13-5Fassembly-5Freport.txt&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=epUg7bSfwCEF_WUOPlT5hPmLXHY7V51Mau09UaQNB5o&e= > > 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 <mailto:Bioc-devel@r-project.org> mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mail >> man_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA >> vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=n5bIFHTIgC1B4EdjWUDLIlVcRJdXScYv >> fbojaqTJZVg&s=IczvesjTwEkPQVlFX5wKSJLUHyjNHE0sk71a-kMAVEI&e= >> > > -- > 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 <mailto:hpa...@fredhutch.org> > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=49jni5SmG_DH80nnPZXXqvFNceB5jkZtlb7eKEA8558&s=g4eW0swjrNpysDJ67do3xLWcLyskjH51X5-x4kMJYDw&e= >-- Hervé PagèsProgram 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 <mailto:hpa...@fredhutch.org> Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=5BrpbmuLSg2cS13gst2oJ-M8PG3kijaxWs3dZkYY8yw&s=NvAaJQhMJpXLBRTOJp4WG11FR4tuCXJ8cfgCdMlv5OY&e=> -- Best, Kasper
-- 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
