search

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
408 stars 118 forks source link

Mapped Reads to Transcripts Are Sometimes Unsorted #42

Closed DarioS closed 7 years ago

DarioS commented 7 years ago

Some BAM output files (sample.transcript.bam) are sorted whereas others aren't, so it causes an issue if samtools index is used immediately after running RSEM.

[E::hts_idx_push] unsorted positions

One third of the BAM files in the dataset I'm working with don't raise such an error, which is strange. They have not been sorted by me. Could RSEM output be made consistent, ideally always sorted?

bli25wisc commented 7 years ago

@DarioS , All 'sample.transcript.bam' should not be sorted. By default, RSEM will not sort bam files. If you want RSEM sort bam files, you can turn on the '--sort-bam-by-coordinate' option.

Hope it helps.