StringeTie Generating Empty Transcript and Gene Counts

[igor]

Hi @KMKLOHONATZ
I searched the forum for the error message and found this post:

Stringtie invalid escape sequence

Hello! I am pretty new to RNA-seq analysis and Galaxy so bare with me. I have a set of RNA-seq files that I have first put through Trimmomatic and then through HISAT2 for alignment. Everything is well until then and I used the appropriate output options in HISAT2 to make the bam compatible with Stringtie. Im running Stringtie and asking it to output Gene Counts, Transcript Counts, Assembled transcripts and Gene abundance estimates. I also provided a GTF file for mouse (mm10). However, for every sample, I get the same standard error: /usr/local/bin/prepDE.py:72: SyntaxWarning: invalid escape sequence ‘-’ RE_COVERAGE=re.compile(‘cov “([-+\d.]+)”’) /usr/local/bin/prepDE.py:75: SyntaxWarning: invalid escape sequence ‘-’ RE_GFILE=re.compile(‘-G\s*(\S+)’) #assume filepath without spaces… Whats more, for some of the samples, Gene abundance estimates and assembled transcripts still turn out ok but Gene and Transcript counts return this error. For other samples, none of the 4 files succeed all returning the same error. Anyone has an idea of what I did wrong?

Does it help?
Consider using featureCounts. It work with your data.
Kind regards,
Igor