I have a set of BAM files from somewhere else which I don't know how they were generated. I have RSEM reference files generated with RSEM (bowtie, gtf, genomic fa). When running rsem-calcuate-expression, I got the following:
rsem-calculate-expression --bam mysample1.bam ~/softspace/reference/RSEM_bowtie_hg19_genes_reference test rsem-parse-alignments /ark/home/mx010/softspace/reference/RSEM_bowtie_hg19_genes_reference test.temp/test test.stat/test KP9-1_Ctl2.bam 1 -tag XM Warning: The SAM/BAM file declares less reference sequences (35) than RSEM knows (41970)! RSEM can not recognize reference sequence name chrM!
The same reference files work well for BAM files generated by HISAT/Cufflinks.
Thanks in advance for your help!