I'm kind of new to rna-seq and I'd like to get tpm values for the transcripts in my study. I'm trying to use RSEM, but I can't get it to work with my .bam files.
I tried rsem-sam-validator on sorted by name .bam files (using samtools), but the following error is generated.
The two mates of paired-end read HWI-ST909:318:C5CEEACXX:8:1101:1075:79829 are not adjacent!
I also tried the convert-sam-for-rsem, but only generating similar errors : Number of first and second mates in read HWI-ST909:318:C5CEEACXX:8:1101:10002:21523's partial alignments (at most one mate is aligned) are not matched!.
Is anyone have an idea how I can solve that?