Question: Deseq2 does not recognize htseq count outputs
0
gravatar for nazaninhoseinkhan
2.8 years ago by
Iran, Islamic Republic Of
nazaninhoseinkhan400 wrote:

Dear all,

I am faced with a strange problem.

Yesterday I run deseq2 on a few htseq count tables in Galaxy and I got the result.

Today when I tried to rerun deseq2 it does not recognize htseq count tables already present in my history.

Can anybody explain the source of this problem?

Thank you in advance

Nazanin

ADD COMMENTlink written 2.8 years ago by nazaninhoseinkhan400
1

Minimally you should add here the commands that you use and the errors that you get. How do you expect us to guess what's going on?

ADD REPLYlink written 2.8 years ago by WouterDeCoster43k

When I want to run deseq2 in Galaxy, htseq count data are not appeared in the input boxes and I cannot run deseq2 at all.

ADD REPLYlink written 2.8 years ago by nazaninhoseinkhan400

Can you give a screenshot of your Galaxy interface?

ADD REPLYlink written 2.8 years ago by e.rempel820

My Galaxy screen shot

ADD REPLYlink written 2.8 years ago by nazaninhoseinkhan400

sorry, I don't see anything. You can upload your screenshot to some public repository and share the link.

ADD REPLYlink written 2.8 years ago by e.rempel820

https://ibb.co/k5Kw45

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by nazaninhoseinkhan400

I see that htseq-count suggests dataset 523, does it also suggest other datasets? E.g. 508?

ADD REPLYlink written 2.8 years ago by e.rempel820

There are 8 htseq counts in my history as well as other outputs like cuffdiff, cufflinks, deseq ,...

But It is so strange that Galaxy only realize the topmost data set (whatever it is).

I have not faced with this problem before.

ADD REPLYlink written 2.8 years ago by nazaninhoseinkhan400

If you are using galaxy, better to inspect the output files and post the error.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by geek_y11k
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