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Chimeric reads hard clipping
Hello, everyone. I got a question without answer after a long exhaustive liaterature search. I am using multiple displacement amplification (MDA) to amplify my samples, followed by 454 sequencing. MDA is well known for the generation of chimera, and therefore chimeric reads. In my dataset, nearly 30% reads are chimeric, estimated by Bowtie 2 aligner. I wonder whether there are some tools can retrieve the mapped domains of chimeric reads only from SAM output. If yes, I think this may break chimeric reads into single mappable reads.
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