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.
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)
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?