STAR+RSEM pippline without gtf
I have question I mapped reads on cds sequence through STAR I don’t have gtf file and want to calculate read count using RSEM but I am stuck by error “RSEM error: RSEM currently does not support gapped alignments” as I don’t have intron so I can not define.
Mapping command: STAR –genomeDir ref/ –runThreadN 4 –readFilesIn R1.fq.gz R2.fq.gz –readFilesCommand zcat –outFilterMismatchNmax 2 –outFileNamePrefix
If anybody suggest me regarding this I will be very thankful.
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