Removing low quality reads

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Removing low quality reads

Getiria Onsongo
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 


shows the results I would like to obtain. 

Data 2 shows the results of Picard tools SAM/BAM Alignment Summary Metrics 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 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: <a href="tel:612-625-0101" value="+16126250101" target="_blank">612-625-0101


Reply | Threaded
Open this post in threaded view
|

Re: Removing low quality reads

Jen Hillman-Jackson
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>
>
>
>
>
> ___________________________________________________________
> 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:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org