hello everyone, I am using nanopore DRS reads to find the m6A sites. I have mapped the reads to reference transcriptome (transcript.fasta from phytozome) so that we get the sites on the basis of transcripts. Now as i see the mapping bam file, all the reads (>99%) are mapped to + strand and very few to negative strand.
(for testing purpose i mapped to genome and found ~equal number of reads mapped to each strand). Also to check the strand of reference transcripts i check the gtf file, it shows equal number on both strands.
so my question is why are the reads mapped only to + strand when mapped to transcript.fasta? Is this have something to do with how the transcript.fasta is made from gtf? do they convert even the - strand transcritps to "+" or forward or sense or 5' to 3' strand?
