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Layla 02-12-2009 08:17 AM

All chromosomes and maq
Hi all,

Has anybody used hg18.2bit from the ucsc genome browser as the reference genome for MAQ? As I cannot give more than one ref.fa file to MAQ, is this the right way to be aligning solexa reads to the entire human genome?


Layla 02-13-2009 08:36 AM

Answering my own question! Not quite sure what the problem with the ucsc hg18 was..but managed to concatenate all the chromosomes into one file, having read a similar query.

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