Sequencing Illumina mate pair libraries beyond 36bp

PNG · 08-06-2009, 10:56 AM

Anyone sequencing mate pair libraries beyond the recommended 36bp?

Thanks,
Phillip

Badger · 03-05-2010, 02:07 AM

Quote:

Originally Posted by PNG

Anyone sequencing mate pair libraries beyond the recommended 36bp?

Thanks,
Phillip

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

Thanks

John_G · 08-24-2010, 12:54 PM

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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08-06-2009, 10:56 AM	#1
PNG Registered Vendor Location: Socal Join Date: Apr 2008 Posts: 6	Sequencing Illumina mate pair libraries beyond 36bp Anyone sequencing mate pair libraries beyond the recommended 36bp? Thanks, Phillip

08-24-2010, 12:54 PM	#3
John_G Junior Member Location: Flagstaff Join Date: Apr 2010 Posts: 1	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.