What are chimeric reads?
4
18
Entering edit mode
6.6 years ago
zhangz.cs ▴ 250

What are chimeric reads? Is there any effective method to distinguish chimeric reads from normal ones? Can someone point me to a survey or reviews on that topic? Thank you a lot!

Zhen

sequence • 39k views
ADD COMMENT
5
Entering edit mode

Linear alignment vs chimeric reads

chimeric reads vs soft clipping vs hard clipping

representative vs supplementary alignment

Multiple mapping

ADD REPLY
0
Entering edit mode

Is there a way of forcing a linear alignment with bwa?

ADD REPLY
1
Entering edit mode
ADD REPLY
39
Entering edit mode
6.6 years ago
donfreed ★ 1.5k

Chimeric reads occur when one sequencing read aligns to two distinct portions of the genome with little or no overlap. Chimeric reads are indicative of structural variation. Chimeric reads are also called split reads.

After aligning with bwa mem, chimeric reads will have an SA tag as described on page 7 of the SAM format specification. To find them all you have to do is extract them using grep.

samtools view my_alignment.bam | grep 'SA:' | less

For reference:

ADD COMMENT
4
Entering edit mode

Also note that chimeric reads are not the same as chimeric genes. In RNA-seq chimeric reads may indicate the presence of chimeric genes but for DNA-seq they often are evidence for structural variation without necessarily being evidence for chimeric gene/transcript events.

ADD REPLY
1
Entering edit mode

In RNA-seq chimeric reads may indicate the presence of circRNAs

ADD REPLY
0
Entering edit mode

What exactly is "structural variation" supposed to mean here?

ADD REPLY
4
Entering edit mode
6.6 years ago
Renesh ★ 2.0k

Chimerism condition in which a gene is formed from combination of two other genes. Suppose part of your gene is matching to one gene ( also of species) and other part is matching to other gene (also can be from different species).

If you want to detect chimerism in your sequence, the simplest way is to match your gene to NCBI or any other database. Then check the alignment hits. If there chimerism exists, part of your gene will match to different genes.

ADD COMMENT
4
Entering edit mode
ADD COMMENT
0
Entering edit mode

The link is broken.

ADD REPLY
0
Entering edit mode
ADD REPLY
3
Entering edit mode
6.6 years ago

Chimeric reads is the sequence form through the combination of portions of one or more coding sequences to produce new genes.

http://scienceblogs.com/digitalbio/2007/02/01/sequencing-a-genome-part-vi-ch/

ADD COMMENT

Login before adding your answer.

Traffic: 1986 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6