Question: What are chimeric reads?
10
gravatar for zhangz.cs
3.6 years ago by
zhangz.cs140
China
zhangz.cs140 wrote:

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 • 19k views
ADD COMMENTlink modified 24 months ago by Shicheng Guo4.7k • written 3.6 years ago by zhangz.cs140
1

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

ADD REPLYlink written 3.6 years ago by Ram15k
23
gravatar for donfreed
3.6 years ago by
donfreed1.2k
Mountain View, CA
donfreed1.2k wrote:

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:

http://www.biomedcentral.com/1471-2164/12/375/

http://www.nature.com/nrg/journal/v12/n5/abs/nrg2958.html

ADD COMMENTlink written 3.6 years ago by donfreed1.2k
3

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 REPLYlink written 3.6 years ago by donfreed1.2k

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

ADD REPLYlink written 12 months ago by syxbestmayer0
3
gravatar for Abdul Rafay Khan
3.6 years ago by
Karachi, PK
Abdul Rafay Khan810 wrote:

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 COMMENTlink written 3.6 years ago by Abdul Rafay Khan810
3
gravatar for Renesh
3.6 years ago by
Renesh1.2k
United States
Renesh1.2k wrote:

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 COMMENTlink written 3.6 years ago by Renesh1.2k
3
gravatar for marina.v.yurieva
3.6 years ago by
Farmington, CT
marina.v.yurieva400 wrote:

A simple explanation:

http://drive5.com/usearch/manual/chimera_formation.html

ADD COMMENTlink written 3.6 years ago by marina.v.yurieva400
2
gravatar for Shicheng Guo
24 months ago by
Shicheng Guo4.7k
Shicheng Guo4.7k wrote:

Linear alignment vs chimeric reads

chimeric reads vs soft clipping vs hard clipping

representative vs supplementary alignment

Multiple mapping

ADD COMMENTlink modified 24 months ago • written 24 months ago by Shicheng Guo4.7k
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