Hi, there, I've generated gtf files with Stringie as been explained in Hisat Stringtie Ballgown paper by pertea 2016 doi: 10.1038/nprot.2016.095 https://www.ncbi.nlm.nih.gov/pubmed/27560171
Now, since ballgown doesn't, currently support TPM, I wanted to use DESeq2 in R to do DE analysis,
First I need to extract reads from Stringie generated gtf files.
I found this nice page that explains how to do that with python script that they also provide: http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#deseq
Now, when I run the python script with -i option and provide the list path to python, or without the list option I get an error
python prepDE.py -i phenotype_2.txt
File "prepDE.py", line 32 print "Error: Text file with sample ID and path invalid (%s)" % (line.strip()) ^ SyntaxError: invalid syntax
The script can be checked here: http://ccb.jhu.edu/software/stringtie/dl/prepDE.py
So it doesn't recognize the list and it doesn't see the folders with gtf files, although it is build according to the paper.
Any suggestions are appreciated, thank you.