Mapping to a custom reference

[LauraR]

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]

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.