RNA-Seq QC for aligned files (bam)

Question

[genomics Newbie]

Hello,

I am trying to find a qc package to be used with.bam files. In using the RNA-SeQC package I ran into difficulty because it required -s, -r, and -r arguments. I only have a .bam file and do not have these required parameters.

Is there a RNA-Seq specific QC tool where I can simply point to the .bam file and have it create a qc report?

Thank you.

[GenoMax]

You can use picards' RNAseq Metrics tool described here.

[lshepard]

Another option, although indirect, is to convert your BAM to FASTQ files with tools such as Picard's SamToFastq, and then run standard FASTQ QC programs like FastQC on the resulting FASTQ files. Just wanted to mention this in case you are unaware.

Edit: this would of course only contain up-stream QC outputs, rather than aligned metrics etc..., but if this is something you need, then it could be useful.

Answer 1

[Friederike]

RSeQC, QoRTs, BamQC are all valid options.

However, I'm surprised you cannot use RNA-seQC, because in its description it says: "RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files."