Hi all,
Has anybody experience with decoding barcoded DNA sequences? We're sequencing PCR amplicons, all identical except for a (custom) 10nt barcode, flanked by transgenic cassettes.
Like this: ----Cassette1---barcode---Cassette2------
So far I've been considering:
1. Generate a custom reference (containing entries for all transgenic cassettes [1,2,etc]) for STAR, but then all (interesting) reads would end up being multimappers. Then postprocess with custom code.
2. Generate a single custom reference with a single barcode. Allow up to x mismatches during alignment (to allow for the different barcodes) and then postprocess the passing reads with custom code.
I'd like to avoid custom-coding (and reinventing the wheel) as much as possible obviously.
Appreciate any ideas. Thanks in advance!
Has anybody experience with decoding barcoded DNA sequences? We're sequencing PCR amplicons, all identical except for a (custom) 10nt barcode, flanked by transgenic cassettes.
Like this: ----Cassette1---barcode---Cassette2------
So far I've been considering:
1. Generate a custom reference (containing entries for all transgenic cassettes [1,2,etc]) for STAR, but then all (interesting) reads would end up being multimappers. Then postprocess with custom code.
2. Generate a single custom reference with a single barcode. Allow up to x mismatches during alignment (to allow for the different barcodes) and then postprocess the passing reads with custom code.
I'd like to avoid custom-coding (and reinventing the wheel) as much as possible obviously.
Appreciate any ideas. Thanks in advance!
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