Hello!
I am trying to join two datasets by (Column 1) using these parameters (attached pic).
The normalized counts file does not have a header for that first column but the “Genes with significant adj p-value & abs(log2(FC)) > 1” file does, which is GeneID. When joining two datasets, how can I keep the first column header in the output file? because it disappears as if the first normalized counts file overwrites the 2nd file header. Thanks in advance!
Hi @Abdulrahman_Alsadiq
The problem is only the file with normalized counts have a header line, while file with DGE results does not have one. Consider adding a header line to the DGE file. Maybe try the following:
Galaxy Upload menu > change to Pate/Fetch Data tab
paste:
GeneID BaseName log2(FC) StdErr Wald-Stats P-val P-adj
Give it a meaningful name, e.g., header.txt (left box above the paste/fetch data box in the upload menu).
in the middle box specify format (datatype) as tabular (type tabular or search for it)
click at Cog wheel icon (Upload configuration) to the risght of the 3d box and tick "Convert spaces to tabs)
Click Start.
Check the uploaded file using mini-preview in the history panel. Make sure the datatype is tabula, and you can see columns with proper content.
Search for Concatenate two files in Galaxy tool panel (type Concatenate into Search/Filter box at the top of the tool panel). Add the header to DGE file usinig Concatenate tool.
Use Join datasets on the new file and normalized counts file. Make sure you set Keep the header lines to Yes.
Hope that helps.
Kind regards,
Igor
