). it seems to be related to the BWA output getting messed up,
with (part of) columns missing or duplicated on some lines.
I have not found a systematic pattern in the errors, they seem to
happen rather random.
On 08/08/2013 05:06 PM, Moritz Juchler wrote:
Dear Galaxy Community,
I
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
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)
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.fasta
I solved it so far :) Thanks for your help.
On 26 July 2013 16:15, Jennifer Jackson j...@bx.psu.edu 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.
2 I also have BWA installed
version, with which I did a succesful alignment?)
Best
Moritz
On 26 July 2013 16:15, Jennifer Jackson j...@bx.psu.edu 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.
2 I also have BWA
at 10:40 AM, Moritz Juchler
juch...@stud.uni-heidelberg.de wrote:
Hey,
now I am having a new problem: Convert SAM to BAM
Tool execution generated the following error message:
[samopen] SAM header is present: 93 sequences.
Parse error at line 106: sequence and quality are inconsistent
:51, Moritz Juchler juch...@stud.uni-heidelberg.dewrote:
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 steps :) I wrote down
* 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, Moritz Juchler juch...@stud.uni
file, and restarted Galaxy?
see also:
http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorialhttp://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
Hope this helps
Hans-Rudolf
On 07/16/2013 08:35 PM, Moritz Juchler wrote:
Hello Ladies and Gentlemen,
I am Moritz
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 installed
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