featureCounts from the subRead package works quite well with cDNA reads aligned to genomic DNA_ref.fa files, but I am having difficulty getting featureCounts to work with cDNA files aligned to the cDNA_ref.fa.
mRatBN7 GTF File:
DNA ref.fa File:
cDNA ref File:
minimap2 used for mapping Nanopore cDNA reads over to the different reference files. The data revealed by samtools flagstat indicates that my cDNA data aligns better to the cDNA?_ref.fa file, and would like to use this data... if only featureCounts would cooperate. But I always get 0.00% reads aligned with the cDNA .
featureCounts( DNA.sam / cDNA.sam, annot.ext = GTF_mRatBN7, isGTFAnnotationFile = TRUE)
It was suggested to me to use
samtools idxstats and using the table directly from there as my gene output, but it doesn't quite feel right.
PS. I have to use R for subReads package as it is not yet fluid with the newer Apple M1 chips, however I do not suspect this is the problem as I experienced this also on Ubuntu terminal.