Running prepare.py on remote server

Question

[suneetamodekurty77]

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!!

[Ram]

1. Use absolute path for everything to ensure you're not making path based mistakes
2. Talk to your university sysadmin
3. Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), 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.
   

[waqaskhokhar999]

You can use featurecounts (http://bioinf.wehi.edu.au/featureCounts/) to generate read count.

[Ram]

OP says

I want to do DeSeq2

Your advice is to

use featurecounts

I don't see how this answers OP's question.

[suneetamodekurty77]

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.

[Ram]

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.

[suneetamodekurty77]

thank you will remember the advise.

Answer 1

[Kristoffer Vitting-Seerup]

You can use the R package tximport specifically look at this section of the vignette (which also explain how to continue with DESeq2 analysis a bit further down). An alternative is the importIsoformExpression() function from my R package IsoformSwitchAnalyzeR which will enable you to find and analyze isoform switches (both in individual genes and genome wide systematic changes).

[suneetamodekurty77]

Got it! Thank you!

[Ram]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work.