Some problem with Stringtie prepDE.py

[Nong510673]

Hi I was preparing the count of string tie for DEseq2 analysis by prepDE.py and when I enter

prepDE.py -i all_gtf_3.txt -v

it turned out to be an error

Error: line should have a sample ID and a file path: sample_1 -e HW.gtf

and I have no idea how to fix it I just enter this domain and just get started not so long.

[BernadetteBiology]

There might be some formatting issues with your all_gtf_3.txt file. Does it look something like this?

sample1 path/to/sample1_merged.gtf sample2 path/to/sample2_merged.gtf sample3 path/to/sample3_merged.gtf sample4 path/to/sample4_merged.gtf