I am currently analyzing RNASeq data obtained from dog cell culture. I used HISAT2 for the alignment to the canis familiaris reference genome in Galaxy. Then, to count the reads, I tried both htseq-count (Galaxy Version 0.9.1) and featureCounts (Galaxy Version 1.6.4+galaxy1). As gene annotation file, I took this file from iGenomes: https://usegalaxy.eu/library/list#folders/Fcf0661b18aa5ad51
It contains 32461 lines, among them 15178 exons (feature type). As I run htseq-count/featureCounts with ‘exon’ as feature type, I expected 15178 lines in the outout of these tools. In contrast, I get both in htseq-count and featureCounts only 2023 lines, even though exons with 0 counts are included in the output.
Do you have any idea what could have happened to the remaining exons?