RSEM error: RSEM can not recognize reference sequence name chrM!

Question

[moxu]

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!

[Devon Ryan]

Are you using a BAM file with genomic alignments?

[moxu]

Not sure. They are supposed to be RNAseq data. If the BAM files were with genomic alignments, what should I do?

Thanks!

[Devon Ryan]

Redo the alignments to the transcriptome that you're using with RSEM

[moxu]

That would be nice but we don't have the fastq files. All we have are the BAM files.

[Devon Ryan]

You can convert them back to fastq with samtools bam2fq.