de novo sequencing of maize (lane and insert size library)

sflong · 10-30-2011, 09:46 PM

we want to sequece a self-cross line of maize, of which repeat sequnces accounts about 70%~80%. we plan to construct mult-insert size libraries, including 300bp, 500bp, 800bp,2000bp,5000bpand 8000bp and utilize 4 lanes to deliver about 50X data using solexa platform. so my question is
1) how to assign different insert size libraries to the 4 lanes?
2) does data of mate pair libraries produce a lot of redudant reads?

thanks a lot!

sflong · 10-30-2011, 09:50 PM

our plan is 300bp--- 1 lane,
500bp--- 1 lane,
800bp--- 1 lane,
2k,5k,8k mixed---1 lane,
I wonder if anybody have better idea for the project?

pmiguel · 10-31-2011, 09:30 AM

I have been wanting to try a DSN normalization method for a genome like maize. Nearly 50% of the maize genome comprises a handful of LTR retrotransposon families. Seems like you could wipe them out with a few cycles of denaturation-annealing followed by DSN.

Then you get a de novo assembly without most of the retrotransposons (which are not going to assemble well anyway using full genome shotgun).

--
Phillip

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10-30-2011, 09:46 PM	#1
sflong Junior Member Location: Hong kong Join Date: Jun 2010 Posts: 8	de novo sequencing of maize (lane and insert size library) we want to sequece a self-cross line of maize, of which repeat sequnces accounts about 70%~80%. we plan to construct mult-insert size libraries, including 300bp, 500bp, 800bp,2000bp,5000bpand 8000bp and utilize 4 lanes to deliver about 50X data using solexa platform. so my question is 1) how to assign different insert size libraries to the 4 lanes? 2) does data of mate pair libraries produce a lot of redudant reads? thanks a lot!

10-30-2011, 09:50 PM	#2
sflong Junior Member Location: Hong kong Join Date: Jun 2010 Posts: 8	our plan is 300bp--- 1 lane, 500bp--- 1 lane, 800bp--- 1 lane, 2k,5k,8k mixed---1 lane, I wonder if anybody have better idea for the project?

10-31-2011, 09:30 AM	#3
pmiguel Senior Member Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008 Posts: 2,317	I have been wanting to try a DSN normalization method for a genome like maize. Nearly 50% of the maize genome comprises a handful of LTR retrotransposon families. Seems like you could wipe them out with a few cycles of denaturation-annealing followed by DSN. Then you get a de novo assembly without most of the retrotransposons (which are not going to assemble well anyway using full genome shotgun). -- Phillip