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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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Clipping and padding reads #110

Open anaklaudia opened 5 years ago

anaklaudia commented 5 years ago

Hi, I mapped paired end reads to transcriptome using star. I use convert-sam-for-rsem to prepare the sam for RSEM but I am getting an error in the validation step that I am not sure how to resolve.

Clipping or padding is detected (cigar S) for read ! RSEM currently doest not support clipping or padding. The input file is not valid!

Thank you for your help on this. A