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-   -   All chromosomes and maq (http://seqanswers.com/forums/showthread.php?t=1196)

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?

Thanks
Layla

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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