RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
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.
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How did you generate the alignments? Did you check the alignment for coordinates that have a negative value in the coordinates?
The RSEM did the alignment by itself using bowtie. It gave warnings in this final steps like mentioned above for multiple reads.