EdgeR error due to counts file not having a header

usegalaxy.org support
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1

Hello,

I am trying to use featureCounts generated counts to perform EdgeR analysis. I manually downloaded all the counts files and added all the samples into separate columns. I am attempting to upload this as a tabular file, but when I upload it, it doesn’t recognize my sample IDs as a header (galaxy generated it’s own header 1, 2, 3, …). How can I manually add a header to the counts that will be recognized by galaxy?

Thank you!

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Hello @ypo

The numbers are just column labels for display, not actually headers.

Try clicking on the “pencil” icon for the dataset and manually designating how many header lines there are (should be 1) on the first tab of the Edit Attributes form, then save.

The format should be similar to the example below. When displayed in Galaxy (“eye” icon), the columns will “right justify” and the column labels will change to match the header line (first line). The columns are tab-separated.

Geneid  sample1  sample2  sample3
gene1         3        4        5
gene2         6        7        8
gene3         9       10       11

Please give that a try. If it doesn’t work, please paste back in the first few lines of your data and we can troubleshoot more from there.

Thanks!