Question: definition of chimeric vs multiple-mapping (SAM)
5
gravatar for Pfs
3.4 years ago by
Pfs490
United States
Pfs490 wrote:

I would like to understand better the difference from a chimeric alignment and a multiple-mapping alignment. From the information in the SAM specifications, it seems to me that a chimeric alignment takes place when the *part* of the query read can map to different places in the reference sequence, whereas a multiple-mapping alignment takes place when the *whole* query read can map to different places in the reference sequence.

Thus, a read can be chimeric if parts of the reads map to the same chromosome but in different places?

 

Thanks in advance.

sequencing alignment • 2.3k views
ADD COMMENTlink modified 3.4 years ago by Devon Ryan86k • written 3.4 years ago by Pfs490
7
gravatar for Devon Ryan
3.4 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

Correct, a chimeric (or "non-linear") alignment occurs when non-overlapping portions of it map to (A) different portions of the same chromosome in a manner not normally biologically supported or (B) to different chromosomes. Multimapping occurs commonly in repeat regions or where there are paralogs. Chimeric alignments occur when there are structural rearrangements, such as with cancer (or something weird happened during sample preparation).

ADD COMMENTlink written 3.4 years ago by Devon Ryan86k
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