I used kallisto genomebam to perform pseudoalignment on stranded single-end and paired-end data and generated bam files. I visualized my bam files on IGV and compared them to the counts I got from kallisto/tximport and they don't match up. Sometimes my count would say 0 but I see reads on IGV or it says there are thousands of reads but I don't see anything on IGV. Has anyone else encountered this issue and resolved it? Also what does the direction of the reads indicate? I have reads that go in the same and opposite direction as my genes. Also, for my stranded paired-end data, why do I have LR and RL reads? I was reading that RL means duplication or translocation; is that always the explanation?
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