Hi Getiria,
Galaxy does not have a tool to do this directly (but it would be a nice
addition). Converting to SAM and using a combinations of tools in Text
Manipulation would likely be possible. It would involve several steps
and some experimentation, but a workflow could be created from that
result to do the filter at all once in the future.
Sorry that we could not help more,
Best,
Jen
Galaxy team
On 10/24/11 9:15 AM, Getiria Onsongo wrote:
Galaxy Users,
I would like to filter a .bam file to remove reads with low mapping
quality, especially ambiguously mapped reads (MAPQ = 0). I can easily do
this using the command line version of samtools as shown below.
samtools view -bq 20 hba1.bam > hba1_MAPQ20.bam
None of the options available under "NGS:SAM Tools" (e.g., Generate
pileup and Filter SAM) provide an option for removing reads with low
mapping quality. The history shown in
http://main.g2.bx.psu.edu/u/onsongo/h/obtaininghighqualityreads
shows the results I would like to obtain.
Data 2 shows the results of Picard tools SAM/BAM Alignment Summary
Metrics
<http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics> on
hba1.bam which contains reads with MAPQ values less than 20. As shown in
this summary html, PF_READS_ALIGNED = 775 and PF_HQ_ALIGNED_READS = 241.
Data 4 shows the results of Picard tools SAM/BAM Alignment Summary
Metrics
<http://main.g2.bx.psu.edu/tool_runner?tool_id=PicardASMetrics> on
hba1_MAPQ20.bam which contains only reads with MAPQ greater than or
equal to 20. As shown in this summary html, PF_READS_ALIGNED = 241 and
PF_HQ_ALIGNED_READS = 241.
Is there a way in Galaxy to filter a bam file to remove low quality
mapped reads similar to using the samtools command line alternative
shown above?
Thanks,
Getiria
--
Getiria Onsongo, Ph.D.
Bioinformatics Research Scientist
Masonic Cancer Center,
University of Minnesota
Minneapolis, MN 55455
Phone: 612-625-0101 <tel:612-625-0101>
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--
Jennifer Jackson
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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