Hi
Greetings
I am trying to run prepDE.py on remote server of my university but
There is an error
python: can't open file 'prepDE.py': [Errno 2] No such file or directory
Please advise an alternative to get the count matrix with stringtie.
I used the -A
option with stringtie and got individual count matrices for each file ( controlled and treated separately) I want to do DeSeq2
How do I proceed?
Please give inputs
Thank you!!
code
option) to present your post better. You can use backticks for inline code (`text` becomestext
), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.You can use featurecounts (http://bioinf.wehi.edu.au/featureCounts/) to generate read count.
OP says
Your advice is to
I don't see how this answers OP's question.
Thank you for the advise. I also read the manual for stringtie and learnt the -A option but my question is,how to get a single gene count matrix for DESeq 2 . I am unable to do that.
Do not add answers unless you're answering the top level question. This content belongs as a reply to waqaskhokhar999 's answer. I'm moving it to a comment on the top-level post now, but please be more careful in the future.
thank you will remember the advise.