Question: Count matrix showing different results than UCSC tracks
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Hello,

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 file1sortedByCoord.bw

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!

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

ADD REPLYlink 11 months ago
ATpoint
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If you are still having trouble tracking why this is different, you can write to us at the GB at genome-www@soe.ucsc.edu (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 11 months ago
Luis Nassar
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