Question: Reconstruct original fragment from paired end reads
0
gravatar for tomaz
3.9 years ago by
tomaz10
tomaz10 wrote:

Hi,

I would like to reconstruct my environemental 16S PCR fragments (slightly more than 300 bp) from my paired end reads (illumina, 250bp). I have good quality reads (more than 200 bp in length) from both ends of the original fragments and they should overlap well to reconstruct the ~300 bp originals. 

Is there a tool in galaxy that would do this job...that is, overlap the two paired ends to make/reconstruct one fragment. If not, what is the best tool available elsewhere to do the job?

I will greatly appreciate any commnets and suggestions!

 

assembly alignment galaxy • 990 views
ADD COMMENTlink modified 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by tomaz10
0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

This tool in the Tool Shed (http://usegalaxy.org/toolshed) will do the job on a local or cloud Galaxy:
http://toolshed.g2.bx.psu.edu/view/lparsons/fastq_join

This is not on the public Main Galaxy instance - and should not be confused with the tools there that either merge the two paired ends into the same dataset or merges the sequence data end-to-end based on common sequence identifiers (or ordering of the input datasets).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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