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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
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alignments with inconsistent mate lengths! #82

Open sommerJY opened 6 years ago

sommerJY commented 6 years ago

Hello, i'm real newbie to RNA sequencing. I was following mapsplice2 - ubu - RSEM pipeline for analysis. I used bowtie-1.1.2 and RSEM-1.3.0 versions.

Though there was no error before the rsem-calculate-expression, i got several warning messages about the difference in read pair

Warning: Detected a read pair whose two mates have different names--HWI-D00574:287:CBPNWANXX:2:2302:8028:90166 and HWI-D00574:287:CBPNWANXX:2:2302:8028:90149!

and then got this error and stopped making the result.

**Paired-end read HWI-D00574:287:CBPNWANXX:2:2302:8028:90166 has alignments with inconsistent mate lengths!

"rsem-parse-alignments Reference/RSEM_REF 30.RSEM/file.temp/file 30.RSEM/file.stat/file RNAseq/21.ubu/file_filtered.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!**

I searched about the former error and found Bo answering "it's okay" but i really don't know how to fix the latter problem......

Is there anybody know how to solve this problem? thanks...

Janesy7429 commented 1 year ago

hello, do you know how exactly can this problem be solved now?