SEQanswers - View Single Post - Bowtie Paired-end options

mrawlins · 10-25-2010, 08:30 AM

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:

Code:

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?

10-25-2010, 08:30 AM	#4
mrawlins Member Location: Retirement - Not working with bioinformatics anymore. Join Date: Apr 2010 Posts: 63	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: Code: 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?