Question: Deseq2 does not recognize htseq count outputs
0
gravatar for nazaninhoseinkhan
21 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan360 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 21 months ago by nazaninhoseinkhan360
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 21 months ago by WouterDeCoster39k

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 21 months ago by nazaninhoseinkhan360

Can you give a screenshot of your Galaxy interface?

ADD REPLYlink written 21 months ago by e.rempel770

My Galaxy screen shot

ADD REPLYlink written 21 months ago by nazaninhoseinkhan360

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

ADD REPLYlink written 21 months ago by e.rempel770

https://ibb.co/k5Kw45

ADD REPLYlink modified 21 months ago • written 21 months ago by nazaninhoseinkhan360

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

ADD REPLYlink written 21 months ago by e.rempel770

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 21 months ago by nazaninhoseinkhan360

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

ADD REPLYlink modified 21 months ago • written 21 months ago by geek_y9.6k
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