Fast flow cells and Allpaths

troendle · 10-31-2013, 08:29 AM

Hi everyone. I'm working on a small fish genome and want to know if anyone is having any success using the new fast flow cells for HiSeq that give >100bp reads as input along with a 3000bp mate pair read as the input for allpaths rather than making the 180bp library. The fast flow cells generate single reads rather than paired reads which is why I'm not sure if this will work. Any input is appreciated especially if you have tried this.

GenoMax · 10-31-2013, 09:16 AM

Quote:

Originally Posted by troendle

The fast flow cells generate single reads rather than paired reads which is why I'm not sure if this will work.

That is not correct. Rapid mode flowcells can generated paired-end reads.

troendle · 10-31-2013, 10:00 AM

Yes they can produce paired end reads but the library that we are attempting to work from is a 450bp library so they would not be overlapping. What we want to know is if allpaths can handle non-paired reads, or if we need to go ahead and make the 180bp library.

GenoMax · 10-31-2013, 11:16 AM

Ok. Your original post was not clear.

You may want to consider running on MiSeq with the new v.3 kits. That can give you 2 x 300 bp reads.

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10-31-2013, 08:29 AM	#1
troendle Junior Member Location: Athens, Ga Join Date: Oct 2013 Posts: 2	Fast flow cells and Allpaths Hi everyone. I'm working on a small fish genome and want to know if anyone is having any success using the new fast flow cells for HiSeq that give >100bp reads as input along with a 3000bp mate pair read as the input for allpaths rather than making the 180bp library. The fast flow cells generate single reads rather than paired reads which is why I'm not sure if this will work. Any input is appreciated especially if you have tried this.

10-31-2013, 10:00 AM	#3
troendle Junior Member Location: Athens, Ga Join Date: Oct 2013 Posts: 2	Yes they can produce paired end reads but the library that we are attempting to work from is a 450bp library so they would not be overlapping. What we want to know is if allpaths can handle non-paired reads, or if we need to go ahead and make the 180bp library.

10-31-2013, 11:16 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,143	Ok. Your original post was not clear. You may want to consider running on MiSeq with the new v.3 kits. That can give you 2 x 300 bp reads.