Question: Count matrix showing different results than UCSC tracks
gravatar for raquelgarza95
15 months ago by
raquelgarza9550 wrote:


I have a bunch of bam files which I converted to bigwigs and put them into a UCSC session. In the UCSC tracks, I can see my samples showing from 6 to 20 reads in "gene 1".

But then when I run featureCounts on them, the gene count matrix tells me that the gene doesn't have any reads...

Am I missing something or if this normal and simply haven't noticed before? If it is normal, why?/how? If not, any advise to fix this?

I should mention that for featureCounts I am using mouse gencode vM20 gene annotation, and I am suspecting UCSC doesn't have the latest patch, could that be it?

Code to convert to bigwig:

samtools sort -o filesortedByCoord.bam file1.bam
samtools index -b file1sortedByCoord.bam
bamCoverage -b file1sortedByCoord.bam -o

Code to run featureCounts:

featureCounts -t gene -F GTF -a annotation.gtf -o gene_count_matrix.csv file1.bam file2.bam file3.bam

Also, it happens in many genes, but I was talking about ENSMUSG00000113203.1 (In case the answer is actually about the annotation patch or something).

Thank you in advance!

ucsc bam bigwig featurecounts mm10 • 427 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by raquelgarza9550

Can you post a screenshot from the IGV where both the bigwig and the original BAM is loaded?

ADD REPLYlink written 15 months ago by ATpoint35k

ADD REPLYlink modified 15 months ago • written 15 months ago by raquelgarza9550

If you are still having trouble tracking why this is different, you can write to us at the GB at (our private mailing list). If you do so, also include a link to the session.

To answer the question about vM20 gene annotations, the latest on the live server is VM18 with VM20 currently on the pipeline. Though I don't believe that's the issue.

ADD REPLYlink written 15 months ago by Luis Nassar390
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