Hello All,
I'm a 2nd year graduate student studying DNA repair. I want to sequence an amplicon library of translocation junctions to quantify the amount of deletions, insertions, and microhomology at breakpoints.
My question is after obtaining the sequencing reads, is it customary to deduplicate reads in the sequencing files? This seems counterintuitive to me since an amplicon based library should contain many identical reads and leave me unable to quantitate different types of junctions.
Any suggestions for packages to use for cleaning these types of reads and/or statistical analysis would be appreciated!
Thanks!
I'm a 2nd year graduate student studying DNA repair. I want to sequence an amplicon library of translocation junctions to quantify the amount of deletions, insertions, and microhomology at breakpoints.
My question is after obtaining the sequencing reads, is it customary to deduplicate reads in the sequencing files? This seems counterintuitive to me since an amplicon based library should contain many identical reads and leave me unable to quantitate different types of junctions.
Any suggestions for packages to use for cleaning these types of reads and/or statistical analysis would be appreciated!
Thanks!
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