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UMMS-Biocore / dolphinnext

A graphical user interface for distributed data processing of high throughput genomics
https://dolphinnext.umassmed.edu
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RNASeq pipeline adapter trimmer unpaired R2 missing #261

Closed lawrencelifshitz closed 4 years ago

lawrencelifshitz commented 4 years ago

Describe the bug If I look at the unpaired/ folder after an a bulk RNASeq pipeline run which used the trimmomatic adapter trimming (eg,/project/umw_michael_czech/WAT_NEW_lml/run2608/work/5d/bdb7216d9cf258b0ccdc39db7755c7/unpaired ) the R2 file is missing. Looking at the command line used, it seems that the same file was specified for the output of both R1 and R2 unpaired data.

To Reproduce I assume any run of the RNASeq pipeline which uses the adapter trimming would have the same problem but I have not checked.

Expected behavior I would think there would be both an R1 and R2 file in the unread/ folder.

onuryukselen commented 4 years ago

Hi Larry, thanks for pointing out this issue. It's fixed for the adapter removal process.