Thanks for sharing http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=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 < geert.vandeweyer2@uantwerpen.be> 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&operation=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

On 09/04/2013 09:59 PM, shamsher jagat 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

--

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.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweye...

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