Really a naïve question but it's a little while I have this one in mind.
From Salmon doc : "If your reads or alignments do not appear in a random order with respect to the target transcripts, please randomize / shuffle them before performing quantification with Salmon."
I don't understand if they are talking about bam and fastq. I understand that a bam can be ordered in different ways but fastq....
But I'm using Salmon in quasi-mapping-based mode on the fastqs. I was wondering if they can be ordererd in a way that need to be shuffled before use with salmon ?
I mean when you download paired-end fastq using sra split-3 option, you will have several R1 & R2 files ordered(how by the way ? ) Same question when you received data directly from your sequencing platform. You pull your different R1 , R2 files separately to use salmon.
Do you need to shuffle the reads in fastq before launching salmon ?
Unless you have a co-ordinate sorted BAM alignment file that you converted to fastq (or you had used a program like
clumpifyfrom BBMap, which re-orders raw reads, when it does de-duplication based on sequence alone), you should not have your reads in any kind of order.