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Forum: Bioinformatics 08-21-2009, 04:53 AM
Replies: 236
Views: 586,504
Posted By Dinny
Hi Anthony, Thanks again for the advice. Taking...

Hi Anthony,
Thanks again for the advice. Taking the reads directly into .bed would be better. The .map converter in Bowtie needs a library file created in Maq, so it would be easier to limit the...
Forum: Bioinformatics 08-20-2009, 04:40 AM
Replies: 236
Views: 586,504
Posted By Dinny
Thanks very much Anthony and ewilbanks. I...

Thanks very much Anthony and ewilbanks.
I looked closer at Bowtie conversion tools and I can create a .map file from the alignment (I'm working with single-end reads), but I have to get Maq working...
Forum: Bioinformatics 08-19-2009, 12:45 AM
Replies: 236
Views: 586,504
Posted By Dinny
Hi all, Thanks for the helpful list. Based...

Hi all,

Thanks for the helpful list. Based on reading the post I've tried out Bowtie to align reads from a ChIP-seq experiment run on Illumina GA-II (the facility gave me non-aligned fastq)....
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