Sorry to send  you again and look forward any input abut joining two overlapping reads Fastq files<div>Thanks</div><div><br></div><div>Kanwar<br><br>
<div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">shamsher jagaut</b> <span dir="ltr">&lt;<a href="mailto:kanwarjag@gmail.com" target="_blank">kanwarjag@gmail.com</a>&gt;</span><br>
Date: Sun, Jan 6, 2013 at 2:24 PM<br>
Subject: joining two FASTq files with overlap reads<br>To: galaxy-user &lt;<a href="mailto:galaxy-user@lists.bx.psu.edu" target="_blank">galaxy-user@lists.bx.psu.edu</a>&gt;<br><br><br>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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<div>Thanks</div>
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<div>Kanwar </div></div><br>
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