Question: FeatureCount output does not match view in IGV browser
gravatar for hosheaa
16 months ago by
hosheaa20 wrote:

I have a BAM file that I view locally in IGV browser. Specifically, I am focused on hsa-mir-122. The viewer shows a count of approximately 2591 for this miRNA in my sample. However, when I use featureCounts tool in Galaxy, it only counts approximately 30. I am not seeing this behaviour with other miRNAs that I look at. I am using hsa.gff3 for counting miRNAs that I mapped using hg38. My primary feature type is "miRNA_primary_transcript" and my GFF gene identifier is "Name". Strand specificity is stranded (forwards).

Can anyone help explain why my featureCounts output is not even close to what I can see when the IGV viewer?

rna-seq alignment galaxy • 494 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 16 months ago by hosheaa20

Hello - We have your email and a request for a shared history was asked for so we can examine the inputs to see what the exact issue(s) may be. I've seen something similar to this before and may be able to help with a workaround (the prior issue was resolved by adjusting usage). Thanks and we can update this post with the generalized solution after review and consider adding more use-case specific help to the tool form if appropriate. Jen, Galaxy team

ADD REPLYlink written 15 months ago by Jennifer Hillman Jackson25k
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Update: the problem was specific to this analysis and is resolved

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k
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