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Old 10-25-2010, 08:30 AM   #4
Location: Retirement - Not working with bioinformatics anymore.

Join Date: Apr 2010
Posts: 63
Default SOLiD Paired-end with Bowtie

This post is really helpful, addressing Illumina mate-pair and paired-end as well as the SOLiD mate-pair. The newest SOLiD machines also have a paired-end, which as near as I can tell is of the configuration:

read1                           read2
-------------->                 <--------------
Now, since the reverse compliment of color-space is the just the reverse sequence, it seems to me this is equivalent to the -fr from bowtie. Has anybody run Bowtie with the SOLiD Paired-end data?
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