Error in prepDE.py after StringTie quantification

Question

[Lorenzo]

Hello, I am doing RNA-seq analysis, using the pipeline suggested here (http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq). I utilized StringTie to map my reads, to assemble transcripts and to estimate transcript abundances. Reading throughout different posts I have decided to use DESeq2 package(count-based methods) for Differential expression analysis DESeq2 instead of Ballgown. Using the following commands:

python2.7 prepDE.py -i merged_list.txt

I obtain the following error:

Error: GTF file not found (/Ballgown/Adrenal_Cortex/)

My working directory is setting in "Prova" while my .gtf file is in "/Prova/Ballgown/Adrenal_Cortex/". The merged_list.txt file contains the ID Adrenal_Cortex in the first column and the path to .gtf file in the second column ("/Ballgown/Adrenal_Cortex/")

How can I solve my problem?

Thank you in advance for your suggestion!

[solomoncharles77]

Try running the command from the directory where /Ballgown is located without specifying the input. Run just python2.7 prepDE.py

[Lorenzo]

Thanks! Now it works. It was too easy. Thanks again!!!