error in deseq2

Question

[anjuraas]

hi I am getting error while running deseq2 in usegalaxy. This is the error:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 14 elements Calls: get_deseq_dataset ... DESeqDataSetFromHTSeqCount -> lapply -> lapply -> FUN -> read.table -> scan

Please help to solve this.

[Kevin Blighe]

Check the formatting of your input file. The parser was expecting 14 columns at row 2, but did not find that. There is likely discrepancy between your header and the main data in the file.

[anjuraas]

I put supress the header option true.

[Kevin Blighe]

Well, check your input file and look for inconsistent formatting. I cannot do that for you from here. Look for, e.g.:

• different numbers of columns
• different field separators (and which field separator is required for Galaxy?)
• presence of 'rogue' DOS / Windows characters, like carriage return

Related to the last point, from where did you obtain your file?

[anjuraas]

I took my dataset from SRA and used bowtie for illumina for alignment and used featureCount for count table. I downloaded gff file and fna file from ncbi.

[Kevin Blighe]

Cool. So, have you checked the first few lines of your input file?

[Kevin Blighe]

Check the input format required by Galaxy and then ensure that your file meets that format.

[anjuraas]

I cant fine anything wrong in featureCount input file. If I give header it is showing duplicate row names are allowed and if I supress the header it is showing the above said error.

[anjuraas]

![this is my feature count table which I used as input for deseq2. I am not able to find the mistake in this.][1]

https://ibb.co/mvk0jCP`

`

[anjuraas]

I ran these same dataset before. that time I got the results. only difference is, now I am using latest version of gff file from ncbi.