Hi I’m new to Galaxy and trying to to perform DEG from RNA-seq for 3 conditions with 3 reps (9 total samples) but have fallen off track by getting empty columns for gene counts at the Stringtie step. The workflow has been FASTQC, Trimmomatic, HISAT2, Stringtie, Stringtie merge, Stringtie (using Stri…

Hi @mlawre The first run through Stringtie was done correctly, the but second run has the problem. This priorr Q&A (and what is linked from it) has the details. Stringtie merge error - #4 by jennaj Please give that a review, and try again. It should solve your problems as well. The parts about ru…

StringTie producing empty column for gene and transcript counts

usegalaxy.org support

jennaj October 30, 2023, 4:16pm 6

Hi @Josh

The instructions are here: Stringtie Merge - #2 by jennaj

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StringTie producing empty column for gene and transcript counts

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