i want to identify differential alternative splicing between two conditions having three replicates each, for that i m using rMATS. I have already generated genome indexes through two pass STAR mapping.
I have three bam files for three control replicates and another three for treated. shall i merge control bam files and also treated bam files and then used the command as:
python rmats.py --b1 merged.bam --b2 merged.bam --gtf gtfFile mygtf --bi STARindexFolder index -od outDir result -t paired -readLength ?
or shall I use
python rmats.py --b1 1.bam 2.bam 3.bam --b2 4.bam 5.bam 6.bam --gtf gtfFile mygtf --bi STARindexFolder index -od outDir result -t paired -readLength ?
Where 1.bam, 2.bam and 3.bam are bam files of controll replicates and 4.bam, 5.bam and 6.bam are bam files of treated replicates.
Also I have a confusion what readLength here means? Is length of fastq reads or something else? If former then how to choose the read length when it might be different for different samples?