Hi there, I have got the .gtf file from stringtie and now I would like to run DEseq2. Unfortunately I should have a count table to use as input for DEseq2 and I actually havn't it. I have tried to us the python script prepDE.py as follows:
python prepDE.py -i myfile.gtf
I have got this error:
Error: Text file with sample ID and path invalid (1 havana transcript 868240 870201 . - . gene_id "ENSG00000230368"; transcript_id "ENST00000432963"; ref_gene_name "FAM41C"; cov "0.0"; FPKM "0.000000"; TPM "0.000000";)
The script can be checked here: http://ccb.jhu.edu/software/stringtie/dl/prepDE.py
Anyone know how to fix it? Thanks in advance
Which python version are you using?
I think is python 2 i think
If you issue
python --version, you will be sure.