Deseq2 error,RNA-seq, usegalaxy

Question

[anjuraas]

hi all i am working in RNA-seq dataset in gastric cancer. i am doing differential expression using DeSeq2 in usegalaxy. While doing i am getting this error

how can i solve this issue? Please help.

[lieven.sterck]

do you by any chance have negative values in your count files? (not sure how this could happen though)

[anjuraas]

i didnt change any of the settings. For i DE when i changed turn off outliers to yes the error was solved. but not to other files

[ATpoint]

Please explain how you preprocessed the data (including code). Did you do any batch correction that changed the raw counts?

[anjuraas]

after aligning with bowtie i took count table from featurecounts.

Answer 1

[skjobs]

The count should not be in negative. The count range from 0 to infinite and not in negative. Please check the input file and remove all negative value into zero.

[anjuraas]

i checked the whole count files. but can't see any negative values. all the values are 0 and >0.

[anjuraas]

Thank you all for your kind replies. I found the mistake in my input file. the deseq tool read my gene name in the count table, which in some cases ended in hash 2 as -2. When I gave another feature type in featurecounts the problem was solved.