Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: ChIP seq : How to map sequencing data that one base is not called?
0
gravatar for sihochoi
4.1 years ago by
sihochoi • 0
Korea, Republic Of
sihochoi • 0 wrote:

I did ChIP-sequencing. During sequencing process, one base was not called due to a problem at the 13 cycle of sequencing.

For Example, CTTCCTGGCCTGNTGCCCCTTGAGGACTCCCAGGTTAGTCCCTGGGCTAGA   You can see it “N” at the 13th base.

I map this data using Bowtie and very few sequence was aligned. 

I thought if I permit more number of mismatch sequence it would increase mapping. 

I tried to change one of parameter in Bowtie : "Maximum number of mismatches permitted in the seed"  from 2 to 3, but it did not work well.

How could I increase mapping with this sequencing data?

 

Best,

Si Ho Choi
ambigiouschars bowtie chip-seq • 1.1k views
ADD COMMENT • link •
modified 4.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.1 years ago by sihochoi • 0
0
gravatar for Jennifer Hillman Jackson
4.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You probably need to adjust other parameters or there are other problems in the data. Maybe -l (seed length) is too high? This could be true if using the default 28 bases and the reference also contains ambiguous characters.

But that is a guess. See the manual here and in the 'Filter' section below it, as it will tell you how to find out why the sequences are being discarded:
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#ambiguous-characters

Thanks, Jen, Galaxy team
ADD COMMENT • link written 4.1 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 183 users visited in the last hour