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Old 08-06-2009, 10:56 AM   #1
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Default Sequencing Illumina mate pair libraries beyond 36bp

Anyone sequencing mate pair libraries beyond the recommended 36bp?

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Old 03-05-2010, 02:07 AM   #2
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Originally Posted by PNG View Post
Anyone sequencing mate pair libraries beyond the recommended 36bp?

I was thinking about doing the same thing as well, has anyone tried this ?

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Old 08-24-2010, 12:54 PM   #3
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Default Mate pair length

I recently did a 101-bp run with indexed mate pairs. Rather than cut out a 300-400 bp chunk at the second fragmentation step, I took a 600 bp chunk. So far, we have not seen any odd bioinformatic results indicating a junction-point issue. That said, you can always just trim the ends if it is of concern. I indexed the mate pair and had it in with 4 other bugs that I prepared as paired end. The mate-pair sample definitely was the cleanest of the group, i.e. better quality scores toward the end of the reads.
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