too many suppressed reads
Hi,
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.
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.