Joining Two Fastq Files With Overlap Reads

Question: Joining Two Fastq Files With Overlap Reads

5.9 years ago by

United States

shamsher jagat • 590 wrote:

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

bwa alignment • 2.1k views

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modified 5.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.9 years ago by shamsher jagat • 590

5.9 years ago by

Makis Ladoukakis • 60

Makis Ladoukakis • 60 wrote:

Dear Galaxy users, I have a tool which among other files it produces certain images in .png format. Does anyone know if there is a way to make them appear inside the "display data" interface? Thank you in advance, Efthymios Ladoukakis

ADD COMMENT • link written 5.9 years ago by Makis Ladoukakis • 60

5.9 years ago by

shamsher jagat • 590

United States

shamsher jagat • 590 wrote:

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

ADD COMMENT • link written 5.9 years ago by shamsher jagat • 590

5.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Kanwar, It is true that the "FASTQ joiner" tool will not "assemble" reads that overlap. But, when using BWA you will not want to do that anyway. Perhaps the problem with the data itself (format or quality score scaling) or the BWA parameters set? There should not be a problem as far as I know with aligning the data, even if it overlaps. The issues that you had aligning just the forward reads seems to be another good indicator that there is more going on. Was this on the public Main Galaxy instance http://main.g2.bx.psu.edu usegalaxy.org)? If so, you can send in a bug report from a failed run or share a history link and we can provide feedback if you are still not sure what the problem is. Thanks! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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