All chromosomes and maq

[Layla]

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

[Layla]

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.