not able to run Deseq 2

Question

[ashwing.kofficial]

Hello everyone, I am not able to run Deseq 2 and I could't figure out where my problem is, I was running Hisat 2, followed by stringtie and string tie merge and another round of string tie , the annotation file I used is gencodev37.gtf, can anyone please tell me where I am going wrong and I'm doing all of this on the galaxy server. I searched for solutions and all I can find is maybe this strg id is a problem but i'm not sure. It would be a great help if you guys can suggest a solution.

[GenoMax]

We have told you before to post questions related to Galaxy on their help forum: https://help.galaxyproject.org/

It is not to discourage you but to ensure that you get specific help from galaxy experts there. They have dedicated support staff that monitor the forum who may be able to look up your data (if you are using PSU galaxy server) and answer specific questions like this one.

[ashwing.kofficial]

I'm sorry, the response is better here , that's why i post it in Biostar but thanks for your advice will follow it .

[Friederike]

1. without an error message it's going to be difficult to help you
2. I'm sure there are standard workflows available on Galaxy involving DESeq2 that do work (they may not use StringTie, but see Genomax's comment for that)

[ashwing.kofficial]

Thanks a lot Friederike, I used feature counts instead of String tie method

Answer 1

[GenoMax]

If you are doing simple RNAseq analysis (not looking for novel transcripts) and are using samples from a genome that has a well characterized transcriptome (e.g. human/mouse) there is no need to do stringtie analysis. You can simply align/count your data and then take those raw counts to DESeq2. That way you will have gene names/ID and counts to simplify things.

[ashwing.kofficial]

Thanks a lot Geno Max, I was able to count my data using feature counts and analyze it using Deseq.

[Friederike]

Please accept the response that was helpful