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Old 01-26-2012, 01:54 PM   #1
Junior Member
Location: Maine

Join Date: Mar 2011
Posts: 2
Default 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!
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