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

On 1/6/13 2:24 PM, shamsher jagat 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


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