gravatar for a.palmer

2 hours ago by

Hi there,

I'm currently analyzing some RNA-seq data, and featureCounts is behaving weirdly.
The problem is that I expect a specific gene (pie-1) to be expressed in my sample, however featureCounts tells me that I have no reads. Though when I input my data into IGV the program shows at least 5 paired reads on my gene.

IGV resultimgur.com/a/qO8mjgN

This is my featureCounts code:

S996_1 <-featureCounts(files="foo.filtered.sorted.bam",
                   annot.ext="Caenorhabditis_elegans.WBcel235.96.gtf",
                   isGTFAnnotationFile=TRUE, GTF.featureType="exon",GTF.attrType="exon_id",
                   isPairedEnd=TRUE, nthreads=12, useMetaFeatures=F,
                   genome="Caenorhabditis_elegans.WBcel235.dna.toplevel.fa",
                   juncCounts = T, allowMultiOverlap=T, reportReads= "SAM", reportReadsPath=NULL)

featureCounts output
imgur.com/a/ESNHlak

I would expect to see at least some reads for this gene, as I expressed it in-vivo as part of my experiments.
For reference I aligned my data with hisat2, filtered it for paired-end reads and sorted it by chromosome position with samtools.

Can somebody please help?

Thanks!

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modified 2 hours ago

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2 hours ago
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a.palmer10



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