draw multiplot of each group

[neptuneyt]

I have two group control:c1.bam\c2.bam\c3.bam and case:t1.bam\t2.bam\t3.bam So how to make configure file,it appears not work as follows: c1.bam:c2.bam:3.bam -1 control t1.bam:2.bam:3.bam -1 case

[bounlu]

I think you can't collapse replicates as 1 group but you can compare them in pairwise manner like this:

t1.bam:c1.bam
t2.bam:c2.bam
t3.bam:c3.bam
t1.bam:c2.bam
t1.bam:c3.bam
t2.bam:c1.bam
t2.bam:c3.bam
t3.bam:c1.bam
t3.bam:c2.bam

or you can merge them first by yourself and then compare:

samtools merge t.bam t1.bam t2.bam t3.bam
samtools merge c.bam c1.bam c2.bam c3.bam

t.bam:c.bam