Diffbind error with different replicate numbers

[alexbisias]

Hi, I’m running diffbind one some ATAC-sequencing data and have been successful when the number of replicates has been equal between my two conditions, but I get an error message when I have, for example, two replicates in one condition and three in the other condition. Could I be doing something wrong or is Galaxy not configured to carry out a 2-vs-3 (or any non-equal-replicates-between-conditions) diffbind analysis? This is the message I get below:

Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in data.frame(SampleID = samples, Condition = groups, bamReads = bams, :
arguments imply diff

Thanks in advance!

If it helps, here is a link to the history in question: the files that were my input are #1-13 and the produced error files are #14-18: Galaxy

[jennaj]

Hi @alexbisias

@alexbisias

Could I be doing something wrong or is Galaxy not configured to carry out a 2-vs-3 (or any non-equal-replicates-between-conditions) diffbind analysis?

It is the second reason. The way the tool form is designed requires that there is a 1-1 relationship between pairs of peak and read bam inputs, and control bam inputs are optional.

Help on the tool form covers more details, this is a summary below. Please scroll down on the tool form to the What it does section for all the help.

Specify the Read BAM files used in the Peak calling. The input order of the BAM files for the samples MUST match the input order of the peaks files.

If specifying a control BAM file, all samples are required to specify one, see Help section below. The input order of the BAM files for the samples MUST match the input order of the peaks files.