Deseq2 error after stringTie gene count are given as input

I have a problem while performing a Deseq2 in galaxy web.

Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
no lines available in input
Calls: get_deseq_dataset → lapply → lapply → FUN → read.table

Hi @Sohailul_Hannan

This error

usually means that one or more of the count input datasets has no content (is empty). Please check for that situation first. If none are empty, then try at least one rerun to eliminate a transient cluster issue from being a factor.

If a rerun fails and the inputs look Ok, you can generate a share link to your history and post that back publicly for review. Or, you can ask for a moderator to start up a private message chat to share it privately instead. How to generate the link: sharing-your-history

Thank you for your assist.

After checking my count input datasets i found that my control 2 and control 4 has no line (empty).

Why they were empty i don’t understand.

May I proceed to next Deseq2 step without selecting Control 2&4 as input?



You should find out why there are no results from the upstream tool. Maybe it can be fixed.

Whether to drop datasets from the analysis is a scientific decision. Just keep in mind that this tool technically requires at least two factor levels and at least two count files per factor level. With a minimum of three per factor level considered best to generate meaningful results.

I have used 6 control (without 2 empty control) and 9 Treated gene count sample file for deseq2 analysis.
I found the result.

Thank you for your help.
I am grateful for your response.

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Glad that helped! :slight_smile: :smiley: :partying_face: