Question: Too many suppressed reads
0
gravatar for Ulduz
5.9 years ago by
Ulduz20
Istanbul
Ulduz20 wrote:

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.

chip-seq • 1.1k views
ADD COMMENTlink modified 5.9 years ago by Manvendra Singh2.1k • written 5.9 years ago by Ulduz20
2
gravatar for Manvendra Singh
5.9 years ago by
Manvendra Singh2.1k
Berlin, Germany
Manvendra Singh2.1k wrote:

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 

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Manvendra Singh2.1k
1

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

ADD REPLYlink written 5.9 years ago by Devon Ryan96k
1

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

ADD REPLYlink written 5.9 years ago by Manvendra Singh2.1k

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

ADD REPLYlink written 5.8 years ago by Ulduz20

Yes, You can go for -n , its seed matching

I work with repetitive elements so I use -v

ADD REPLYlink written 5.8 years ago by Manvendra Singh2.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 685 users visited in the last hour