Hi Galaxy users! I'm attempting to call variants from targeted amplicon sequencing, and ran MPileup on my collection of Bowtie2 aligned reads. The sample names (which were the file names) were replaced in the Mpileup output by "local_bam_0.bam, local_bam_1.bam, local_bam_2.bam...", and I'd like to relabel with my original sample IDs. What is the order in which files are fed into Mpileup when bams are submitted as a collection? Would it be the order they appear in the collection? Alphabetical perhaps?
As a bonus question, what would I have needed to do in order to preserve the sample IDs in the first place?
Any info would be appreciated, thanks!