Chimeric reads analysis

Question

[biobiu]

Hello, I want to map reads against (a very small) reference with the goal to identify reads that are chimeric (e.g mapped to two different "chromosomes" as a result of recombination) and the recombination site itself. My plan is to either trying to find chimeric read by analyzing of clipped reads, or using bowtie in local mode and writing some code to analyze the SAM file. Does anyone have better recommendations? The chimeric read will be one read of the paired-end reads if that affect your suggestions. Thank you!

[i.sudbery]

I have done the same when trying to identify chimeric reads.

[biobiu]

Thank you. When you say the same do you mean that you looked for clipped reads or analyzed local alignments? Thanks!

[i.sudbery]

From what I remember, we did both.