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.