Bam Qc And Coverage

Question: Bam Qc And Coverage

5.2 years ago by

United States

shamsher jagat • 590 wrote:

I am looking for a tool to perform QC of Bam file especially following functions: 1. BAsic information and stat. 2. Coverage across reference features- gene/ transcripts. Is it possible to do it in Galaxy? Thanks

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modified 5.2 years ago by Joachim Jacob • 50 • written 5.2 years ago by shamsher jagat • 590

5.2 years ago by

Geert Vandeweyer • 20

Geert Vandeweyer • 20 wrote:

I've added our BAM-QC/Coverage tool to the toolshed. Search for 'coverage_report' http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&ope ration=view_or_manage_repository&id=5616f9aed501df32 It generates a pdf plot similar to the attached one (full exome set, but only a few genes in bed file for demo purposes). Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

ADD COMMENT • link written 5.2 years ago by Geert Vandeweyer • 20

Thanks for sharing http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&ope ration=view_or_manage_repository&id=5616f9aed501df32 I was wondering how can I use this tool on tool shed or too shed are resources only to download and use at their own. Thanks for your help. On Thu, Sep 5, 2013 at 12:24 AM, Geert Vandeweyer <

ADD REPLY • link written 5.2 years ago by shamsher jagat • 590

5.2 years ago by

Joachim Jacob • 50

Joachim Jacob • 50 wrote:

Hi Shamsher, Another alternative is to use bamqc from the qualimap suite. The wrapper you can find at: http://toolshed.g2.bx.psu.edu/view/joachim-jacob/qualimap_suite You need to install this tool in a local Galaxy, with the qualimap suite installed and perl (see README). Cheers, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

ADD COMMENT • link written 5.2 years ago by Joachim Jacob • 50

Joachim , Thanks that is exactly I was looking as Qualimap is exhausting memory. Thanks Geert. On Fri, Sep 6, 2013 at 12:32 AM, Joachim Jacob | VIB | <joachim.jacob@vib.be <="" div="">

ADD REPLY • link written 5.2 years ago by shamsher jagat • 590

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