Question: How to get raw reads from bam file
0
gravatar for michellek
4 months ago by
michellek0
michellek0 wrote:

Hi,

I can't figure out how to get raw reads counts from a bam file. I have 3 different experimental conditions and trying to get an MDS plot that includes all three. Therefore I need the raw read counts. How do I get this?

Michelle

rna-seq galaxy bam • 133 views
ADD COMMENTlink modified 4 months ago by Devon Ryan1.8k • written 4 months ago by michellek0
0
gravatar for Devon Ryan
4 months ago by
Devon Ryan1.8k
Germany
Devon Ryan1.8k wrote:

You'll want to use featureCounts, which is available in Galaxy. You'll need to provide it with your BAM file and an annotation in GTF format so it knows where your genes/exons are.

ADD COMMENTlink written 4 months ago by Devon Ryan1.8k
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