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.
What are chimeric reads?
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
• 64,852 views
•
link
updated
by
Ram
•
written
by
zhangz.cs •
•
written
by
zhangz.cs •
4 answers
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:
In RNA-seq chimeric reads may indicate the presence of circRNAs
• 0 views
•
link
written
by
syxbestmayer •
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.
A simple explanation: http://drive5.com/usearch/manual/chimera_formation.html
• 0 views
•
link
updated
by
Ram
•
written
by
marina.v.yurieva
•
written
by
marina.v.yurieva
possibly here now https://drive5.com/usearch/manual/chimeras.html
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/
• 0 views
•
link
updated
by
Ram
•
written
by
Abdul Rafay Khan
•
written
by
Abdul Rafay Khan
Log in to answer this question.
More posts like this
-
Understanding Supplementary reads.
written by kiran •
-
Calculating Effective Population Size from One Individual
written by jsweet6 •
-
Tools for scRNAseq
written by wenbinm •
-
Viewing chimeric reads on IGV
written by heir_of_isildur88 •
-
How is a deletion with inserted bases simulated?
written by zhangz.cs •
-
What is a repetitive region?
written by zhangz.cs •
-
Difference Between Somatic And Germline Variant Calling?
written by William
-
How To Distinguish Chimeric Transcript From Fusion Gene
written by upendrakumar.devisetty
-
Coverage-Based Search In Tophat
written by jeremy
-
How To Evaluate 454 Sequences
written by Sashi Kiran Challa
This might be relevant: http://scienceblogs.com/digitalbio/2007/02/01/sequencing-a-genome-part-vi-ch/
Linear alignmentvschimeric readschimeric readsvssoft clippingvshard clippingrepresentativevssupplementaryalignmentMultiple mappingIs there a way of forcing a linear alignment with bwa?