What are chimeric reads?

Question

[zhangz.cs]

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

[Shicheng Guo]

Linear alignment vs chimeric reads

chimeric reads vs soft clipping vs hard clipping

representative vs supplementary alignment

Multiple mapping

[ricardoguerreiro2121]

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

[Ram]

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

Answer 1

[donfreed]

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:

• Identification of genomic indels and structural variations using split reads
• Genome structural variation discovery and genotyping

[donfreed]

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.

[syxbestmayer]

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

[Dunois]

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

Answer 2

[Renesh]

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.

Answer 3

[marina.v.yurieva]

A simple explanation: http://drive5.com/usearch/manual/chimera_formation.html

[zx8754]

The link is broken.

[cmdcolin]

possibly here now https://drive5.com/usearch/manual/chimeras.html

Answer 4

[Abdul Rafay Khan]

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/