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Kingsford-Group / ribomap

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Stranded RNA-Seq on opposing strand #8

Closed nickstiffler closed 6 years ago

nickstiffler commented 7 years ago

Hi, Our RNA-Seq protocol results in fragments that align to only the opposite strand of the transcript, but the riboseq reads align to the forward strand. Your pipeline assumes stranded reads will always align to the forward strand. I have made a change to the library type of salmon in the run_ribomap.sh script, so I am able to process my data, but I thought I should bring this up so additional options could be added to ribomap in future releases to accommodate this. Thanks.

Nick

ckingsford commented 7 years ago

Thanks! This is a good point. We'll try to add this in a future release of ribomap.

hadjie01 commented 4 years ago

Hello! I am trying to do the same because my RNA-Seq data is on the opposite strand (SR). Could you please let me know what type of modifications I'll need to do to the script? Thanks a lot!!