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LauraR 01-26-2012 01:54 PM

Mapping to a custom reference
I have whole genome sequencing data (HiSeq, 100 bp paired end, 20X coverage, mouse genome) that I'd like to map to a custom reference of about 14.5 Kb. Tools like BWA are designed for large reference genomes. Does it make sense to attempt an alignment using BWA? I have access to Galaxy Tools and Genome Quest. Thanks!

chencheni 01-26-2012 03:01 PM

yes. i think bwa is better. if you are working on the mouse genome, while not try to align the sequence to the full genome at first , and then cut the appropriated region you needed. The result will be better than it you mapping to reference sequence directly.

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