Unidentified error running goseq

1

I’m doing gene enrichment analysis using goseq. The two input files for this were generated by following the instructions from 3: RNA-seq genes to pathways.

I keep getting the following error and I’m not sure what is the matter:

  • { “code_desc”: “An undefined error occured, please check your input carefully and contact your administrator.”, “desc”: “Fatal error: An undefined error occured, please check your input carefully and contact your administrator.”, “error_level”: 3, “match”: “Error in”, “stream”: “stderr”, “type”: “regex” }

Could it be that I picked the wrong GeneID format? I picked Entrez ID, as the tutorial suggests, but Ensembl ID was the default option…

Assistance would be appreciated :slight_smile:

2

Hi @Kanishk,
can you share your history with me? I’ll have a look at it. I sent you my email by private message.

Regards

1 Like
3

Hi @gallardoalba,

I have shared this history with you now. Please let me know if there’s something I can fix in my inputs to make the program run.

Thanks!

4

Hi,
I’ll check it today.

Regards

1 Like
5

Hi @Kanishk,
as I indicated to you in the email, you need to remove the version suffixes (so, you should use ENSG00000168209 instead of ENSG00000168209.6) and the headers.

Regards

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6

Thank you!

7

How do you remove the suffixes and headers without having to go and delete each one

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8

Hi, Still having trouble with Goseq and wondering how to remove the version suffixes? any help would be greatly appreciated!!