Removing low quality reads
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
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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Getiria Onsongo -
Jennifer Jackson