Aligning Chimeric Reads

[rfilbert]

Hi there,

Which aligners can handle chimeric reads? I see several threads about this but I can't find an answer.

Thanks!
Robert

[shi]

Dear @rfilbert,

If you have paired-end read data, you may try our Subread aligner (http://subread.sourceforge.net).

When running in paired-end mapping mode, Subread will firstly try to map the paired-end reads to the same chromosome and map them to locations where the paired-end distance criteria are satisfied. However, if these criteria can not be met, Subread will map them as individual reads. This will enable the chimeric fragments, which have their two ends originating from different chromosomes, to be mapped and reported. So if there are chimeric fragments in your data, you should be able to find them in the mapping output.

Best wishes,
Wei