Too many suppressed reads

Question

[Ulduz]

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.

Answer 1

[Manvendra Singh]

You are asking 3 mismatches and one alignment per read, that's 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

[Devon Ryan]

-v is mutually exclusive with itself? I assume that's a typo :)

[Manvendra Singh]

It was funny. Thanks for pointing out. I edited it

[Ulduz]

In different tutorials I have seen they are using n mode for aligning? why are you preferring v mode?

[Manvendra Singh]

Yes, You can go for -n, it's seed matching

I work with repetitive elements so I use -v