Sorry to send you again and look forward any input abut joining two overlapping reads Fastq files Thanks
Kanwar ---------- Forwarded message ---------- From: shamsher jagaut <kanwar...@gmail.com> Date: Sun, Jan 6, 2013 at 2:24 PM Subject: joining two FASTq files with overlap reads To: galaxy-user <galaxy-user@lists.bx.psu.edu> 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. Thanks Kanwar
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