I am new to the field.
So during analyzing my ChIP-seq results I realized in some of my samples only 50% of my reads are uniquely aligned and around 30-40% of my reads are suppressed reads! Suppressed reads contain reads which are aligned to more than one region on genome.
For aligning I am using bowtie which -m 1 and -n 3! and it is doing best and trying hard to align the reads to genome.
Is there any problem with my aligning commands?
P.S.: I would be grateful if you could tell me what commands are you using for aligning your reads in ChIP-seq samples.
you are asking 3 mismatches and one allignment per read, thats why most of them are suppressed
I use these options
-q -v 1 -m 2 --sam --best --strata
-v is mutually exclusive with -n so you can choose one option