HISAT2, Stringtie,DEseq2 differential gene expression

Question

[sanchi.andrea]

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

[h.mon]

Which python version are you using?

[sanchi.andrea]

I think is python 2 i think

[h.mon]

If you issue python --version, you will be sure.

Answer 1

[Devon Ryan]

Read the usage carefully. The -i option is described as follows:

the parent directory of the sample sub-directories or a textfile listing the paths to GTF files

So you need a text file with the name of the GTF file in it or the directory name that has the stringTie results.

As an aside, since you have human data there is unlikely to be any benefit to using stringTie. Either use something like featureCounts or salmon/kallisto.

[sanchi.andrea]

I have tried putting directly the directory as follows:

python prepDE.py -i /media/andrea/Andrea/myfile.gtf

The error is the same:

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";)

My python version is: Python 2.7.15rc1

thanks for any suggestions

[Devon Ryan]

Try actually reading my reply.

[sanchi.andrea]

UPDATE: i fix the problem creating a txt file with tthe name of my file and then the path. Thanks

[grant.hovhannisyan]

You can accept @Devon's answer so everyone knows that your issue is solved