RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
0
0
Entering edit mode
9 weeks ago
kat.bi • 0

I'm running RSEM for obtaining the final files of genes, isoforms and logs, etc. But it throws error as below after processing all rsem steps at rsem-run-em stage.

Warning : The alignment of read AP7290010:11081149 to transcript 8707 starts at -296 from the forward direction, which should be a non-negative number! It is possible that the aligner you use gave different read lengths for a same read in SAM file. ...rsem failed! Plase check if you provide correct parameters/options for the pipeline!

This occurs only for some samples.

Please suggest a solution to resolve this soon.

genomics transcriptome rsem ngs • 1.0k views
ADD COMMENT
0
Entering edit mode

How did you generate the alignments? Did you check the alignment for coordinates that have a negative value in the coordinates?

ADD REPLY
0
Entering edit mode

The RSEM did the alignment by itself using bowtie. It gave warnings in this final steps like mentioned above for multiple reads.

ADD REPLY

Login before adding your answer.

Traffic: 1662 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6