treff: Re: [galaxy-dev] Map with BWA results in correpted SAM file
> >
> > to add on this :
> >
> > we have similar issues (sam-to-bam conversion fails with similar
> > errors). it seems to be related to the BWA output getting messed up,
> > with (part of) columns mi
08/2013 05:06 PM, Moritz Juchler wrote:
Dear Galaxy Community,
I have a local instance and installed 0.5.9-r16 BWA and the toolshed
wrapper. The mapping is successful. I then use the Filter Sam Tool on the
sam file from the alignment, but it spits out this error:
Dataset 26: Filter SAM on dat
Dear Galaxy Community,
I have a local instance and installed 0.5.9-r16 BWA and the toolshed
wrapper. The mapping is successful. I then use the Filter Sam Tool on the
sam file from the alignment, but it spits out this error:
*Dataset 26: Filter SAM on data 24*
Tool execution generated the followi
Hello Galaxy Team,
I get this error
> "Error reading bam file. This usually indicates a problem with the index
> (bai) file. ArrayIndexOutofBoundsException: 6921 (6921)."
when I finish my pipeline and try do view any of the sam or bam files.
-occurs on both hg19 and hg_g1k_v37
-i tried to sort
Hey,
1 I installed Galaxy locally.
2 I also have BWA installed and then used the
3 shed repository to get the bwa wrapper.
4 I have the reference genome
now I'm stuck with the calculate SA coordinate. Segmenation fault.
Google tells me that it could be a problem with
-space (I have 4GB left)
-the
rrent
version, with which I did a succesful alignment?)
Best
Moritz
On 26 July 2013 16:15, Jennifer Jackson wrote:
> Hi Moritz,
>
> Pls see below
>
> On Jul 26, 2013, at 6:37 AM, Moritz Juchler <
> juch...@stud.uni-heidelberg.de> wrote:
>
> Hey,
>
> 1 I inst
I solved it so far :) Thanks for your help.
On 26 July 2013 16:15, Jennifer Jackson wrote:
> Hi Moritz,
>
> Pls see below
>
> On Jul 26, 2013, at 6:37 AM, Moritz Juchler <
> juch...@stud.uni-heidelberg.de> wrote:
>
> Hey,
>
> 1 I installed Galaxy locally.
&g
Hey,
1 I installed Galaxy locally.
2 I also have BWA installed and then used the
3 shed repository to get the bwa wrapper.
4 I have the reference genome:
> -rw-r--r-- 1 trr users 10509 2013-07-25 11:31 human_g1k_v37.dict
> -rw-r--r-- 1 trr users 3153506519 2013-07-25 11:28 human_g1k_v37.fast
Hello Ladies and Gentlemen,
I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
have to setup Galaxy to find SNP's in genomes from hcc patients. I have a
64-bit openSuse 11.3 server on which I installed Galaxy locally, since we
have a) very large files (>30GB per pati
in()
File "/home/trr/galaxy-dist/tools/samtools/sam_bitwise_flag_filter.py",
line 137, in main
flags = int( fields[flag_col] )
IndexError: list index out of range
So here is my 3rd question: How to solve this error? I didnt find anything
online.
Best
Moritz
On 22 July 2013 16:54, Pe
tep I did before was:
7: *Map* with BWA for Illumina on data 5 and data 3: mapped reads
~21,000 lines, 94 comments
format: sam, database: hg19
BWA Version: 0.7.5a-r405 BWA run on paired-end data
That one seems to work correctly.
Any help appreciated :)
Best
Moritz
On 22 July 2013 11:20, Morit
tz
On 17 July 2013 09:51, Moritz Juchler wrote:
> Hey,
>
> no thats correct I did not use Tool Shed. If I would use it, could I skip
> all these manual steps? Is the installation of BWA with Tool Shed also this
> complicated or is it more simle?
>
> How did you not follow my
tarted Galaxy?
>
>
> see also:
> http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorial<http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial>
>
>
>
> Hope this helps
> Hans-Rudolf
>
>
>
>
>
> On 07/16/2013 08:35 PM, Mo
Hello Ladies and Gentlemen,
I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I
have to choose a bioinformatic pipeline management tool to find SNP's in
genomes from hcc patients. My decision was made in favor of galaxy. I have
a 64-bit openSuse 11.3 server.
I have inst
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