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Old 02-12-2009, 09:17 AM   #1
Layla
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Default 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?

Thanks
Layla
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Old 02-13-2009, 09:36 AM   #2
Layla
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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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