Group HTseq counts

Hi. I am doing an RNA-seq study and I want to group in a single file all the counting data of my six samples obtained with HTseq, to be able to visualize them all together. Is there any tool in Galaxy to do this? Thank you.

Hi @julieta, I haven’t run htseq-count in a while, but I think this will work.

The Setup
htseq-count produces a two column output. The first column is the feature name (from the GFF) and the second is the overlap count. This is shown for all features, even if there are 0 overlaps.

Where to Look
For questions where you have multiple datasets, with a common column, and you want to unite them into a single file, start with these two toolboxes in the tool panel (on the left): Text Manipulation and Join, Subtract and Group.

What tio do (I think)
The first thing with promise under Text Manipulation is Multi-Join, and I think his will work. Pick one of your htseq-count outputs as the File to Join and then select the rest in the Add additional file list.

Common key column is 1
Column with values to preserve is 1 and 2
Add header line to the output file is yes
Input files contain a header line is yes (mine did)

You can then use the Text Manipulation → Cut operator to rearrange the columns.


Hi. I have already found the solution. My files are actually collections (sorry I did not say it before), so I went to “Collection Operations” -> “Column Join on Collections”. Anyway thank you very much for your answer.


Hi, I tried Multi-Join and I am having problems with the headers.
The head line of the data sets to merge are: “Geneid” and “Bowtie2 on data 10: aligned reads (BAM)”.
The key is Geneid.

I’ve tried multiple options to merge all frames and I cant keep the header to identify each sample. It gives me this dataset_31867548_V2 that I cannot associate to a sample.

Do you know how to solve this?

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The help text on the tool form uses the “Add header line to the output file”, which usually is enough information to sort out what the output columns represent. From there, you could create a custom header and replace it using other Text Manipulation tools if needed/wanted.

Please give that option a try.

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