Sorry to send  you again and look forward any input abut joining
two overlapping reads Fastq files


---------- Forwarded message ----------
From: shamsher jagaut <>
Date: Sun, Jan 6, 2013 at 2:24 PM
Subject: joining two FASTq files with overlap reads
To: galaxy-user <>

I have a data generated from Miseq 2X250 bp these reads are overlap, before
aligning to a my custom bacterial genome, I have to join these two mate
pair Fastq files and then use BWA alignment tool. I am aware of COPE/ FLASH
can be used. I am looking for if there are similar tool or any way I can
join two Fastq files which i can use for alignment. Just to clarify further
with overlapping reads as such BWA is not aligning the reads. I have used
both as mate pair or used only forward reads to align to genome. The idea
is to find SNPs in different samples.


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