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!