My 454 data contains 20% reads with >1 hits in Bowtie 2. These reads were extracted by samtools. Are there any tools that can be use to make these multi-hit reads become single-hit reads?
I have examined almost all programs for chimeric read or SV detection, and it seems all of these programs have no option to do the job described above. I wonder if same tools, like samtool or bedtool, can do this job.
Many thanks!
I have examined almost all programs for chimeric read or SV detection, and it seems all of these programs have no option to do the job described above. I wonder if same tools, like samtool or bedtool, can do this job.
Many thanks!
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