Question: Bam Qc And Coverage
0
gravatar for shamsher jagat
4.9 years ago by
United States
shamsher jagat590 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
galaxy • 1.7k views
ADD COMMENTlink modified 4.9 years ago by Joachim Jacob50 • written 4.9 years ago by shamsher jagat590
0
gravatar for Geert Vandeweyer
4.9 years ago by
Geert Vandeweyer20 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 COMMENTlink written 4.9 years ago by Geert Vandeweyer20
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 REPLYlink written 4.9 years ago by shamsher jagat590
0
gravatar for Joachim Jacob
4.9 years ago by
Joachim Jacob50 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 COMMENTlink written 4.9 years ago by Joachim Jacob50
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 REPLYlink written 4.9 years ago by shamsher jagat590
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 124 users visited in the last hour