Question: How to get raw reads from bam file
0
gravatar for michellek
9 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

ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by michellek0
1
gravatar for Devon Ryan
9 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k 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 9 months ago by Devon Ryan1.9k

For anyone having trouble with the Featurecounts tool recognizing BAM/GFT inputs, please know that the tool now requires that the database metadata assignment is made to both the BAM and GTF inputs (when sourced from the history).

Please see this post for full details: https://biostar.usegalaxy.org/p/24154/#28027

ADD REPLYlink written 9 days ago by Jennifer Hillman Jackson25k
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