I want to calculate the read counts mapping to repeats in my RNA-seq data. I mapped the reads using Bowtie2 to indices of repeats from UCSC Repeatmasker track in fasta format. Next, I have to calculate the read counts per repeat type, so I tried with featureCounts tool (in Galaxy server). But the output gives me zero counts for all the repeat types.
¿Any ideas? I thought maybe some IDs or columns are not matching but I don't know.
Thank you very much in advance, Gema