Coverage Plot For Rnaseq

Question

[mad.cichlids]

Hi, All

My apologize is this question is too simple to ask here. I was reading this post RSeqQC and RNA-SeqQC - quality control software for RNA-Seq data on making plots about the coverage of the rnaseq alignment bam file. I tried to use another program RSeQC, but I had a hard time to install it on my computer.

It seems RNA-SeQC could also do the job I need. However when I browsed through the picard and gatk website, i did not really see this functionality on either website. Could you give some hints on how to run RNA-SeQC in either picard or gatk?

Best,

Answer 1

[Ido Tamir]

You did not find anything in gatk and picard because its a different program _building_ on gatk and picard functionality. They "forgot" the link to the download site. You have to create and account and log in there then you can download it from http://www.broadinstitute.org/cancer/cga/rnaseqc_download

[mad.cichlids]

Thank you, really appreciate it!