Question: error in deseq2
0
gravatar for anjuraas
10 months ago by
anjuraas10
anjuraas10 wrote:

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.

mirna deseq2 • 303 views
ADD COMMENTlink written 10 months ago by anjuraas10

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.

ADD REPLYlink written 10 months ago by Kevin Blighe60k

I put supress the header option true.

ADD REPLYlink written 10 months ago by anjuraas10

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?

ADD REPLYlink written 10 months ago by Kevin Blighe60k

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.

ADD REPLYlink written 10 months ago by anjuraas10
1

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

ADD REPLYlink written 10 months ago by Kevin Blighe60k

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

ADD REPLYlink written 10 months ago by Kevin Blighe60k

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.

ADD REPLYlink written 10 months ago by anjuraas10

![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`

`

ADD REPLYlink modified 10 months ago • written 10 months ago by anjuraas10

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.

ADD REPLYlink written 10 months ago by anjuraas10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1617 users visited in the last hour