Decoding DNA barcodes within PCR amplicons

[analog900]

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!

[avierstr]

Not 100% clear what you want ?
Do you want to split your reads based on the "internal" barcode, and than postprocess the reads with the same barcodes separately ?

If that is the case, I have a python 3.5 script that can search for partial sequence in a sequence (fasta or fastq) and writes them in separate files.

[fanli]

QIIME's split_libraries_fastq.py script can probably do what you want. You can pretty easily create an index FASTQ file of your 10nt barcodes, if you don't already have one.

[analog900]

QIIME's split_libraries_fastq.py script can probably do what you want. You can pretty easily create an index FASTQ file of your 10nt barcodes, if you don't already have one.

Thanks! This might just work. I'll look into it. Thanks again! Appreciate it!