Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
Best Way to make Mate-Pair library? Manna Sample Prep / Library Generation 10 08-06-2013 03:14 PM
Which cloumn to take from SV Detect to make bed format to make it running on BEdtools vishal.rossi Bioinformatics 1 05-16-2013 03:59 AM
How to make HiSeq indexed paired-end library with homemade oligos? ostrakon Illumina/Solexa 6 03-16-2012 04:22 AM
sanger end-seuqencing of metagenomic fosmid library plumb Metagenomics 0 08-04-2011 09:39 AM

Thread Tools
Old 03-31-2014, 01:33 AM   #1
Location: haifa israel

Join Date: Jun 2011
Posts: 62
Default Best way to make metagenomic library

We have several samples of DNA sampled from the ocean and want to make metagenomic libraries for a Illumina 150PE run. We are debating between doing overlapping reads or an insert size of 400-500bp.
Our end goal is to identify particular genes of interest (estimated to be present in 20-50% of the bacterial population of the ocean).

The way I see it - the pros of overlapping reads is that a 150PE run will give us reads of ~250bp after you merge the L and R side, and that is more easily blastable. The cons are data wasted and more difficulty assembling. The pros of a reasonable sized insert are that the PE data are likely easier to assemble, but you get less info per fragment that is blastable, and I am uncertain as to our ability to get a meaningful assembly (ie will assembly be so fragmented that it will likely not assemble our gene and we will end up having to identify unassembled fragments).

Many thanks for everyone's insights!
Noa is offline   Reply With Quote

assembly, bioinformatics, gene identification, illumina, metagenome

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:20 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO