FeatureCounts creating multiple summary tables

[mbje]

I am trying to analyze some RNA-seq data. I imported pair-end data from NCBI using fasterq-dump, filtered with fastp then performed a bowtie2 alignment on this. I then used the feature counts tool which gives me a tabular output of 7 columns (gene id, location, start, end, strand, length, sample # count). However, instead of having a table where the counts for all of my samples are summarized in separate columns (i.e. gene id, location, start, end, strand, length, sample #1, samples #2, samples #3 etc) I get a separate table for each sample. I want to avoid having to download and copy paste the last column of each table together to get a useable document with data for all my samples. Is there way to get feature counts to give me a single summary table containing the data for all of my samples?

Thank you for your help!

[jennaj]

Hello @mbje

For your question here

@mbje

However, instead of having a table where the counts for all of my samples are summarized in separate columns [..] I get a separate table for each sample.

Is there way to get feature counts to give me a single summary table containing the data for all of my samples?

The original tool outputs individual files but you can combine the results into a table in Galaxy! We have an example in this tutorial. The processing is just a single post-processing tool that can be included in a workflow, or run directly.

• Hands-on: 1: RNA-Seq reads to counts / 1: RNA-Seq reads to counts / Transcriptomics (create-count-matrix)

As you probably know, some downstream tools will expect individual count files and some prefer a table. Getting either is possible!

Please let us know if this helps or if you have follow up questions!