Question: Degenerate primer removal tool on Galaxy?
0
gravatar for shortridge.15
2.9 years ago by
shortridge.150 wrote:

 

Hi there,

I am working on a next generation sequencing dataset and can't seem to find a tool on Galaxy despite extensive searching that can handle degenerate primers. I would like to remove them from my dataset as part of the cleanup steps. Does anyone know of a tool that can do this? P.S. I program in Python (but also somewhat in Perl and R) so writing a script is a possibility, but I am running Galaxy to help with sharing data and analyses with collaborators.

Thanks so much!

Meg

tool primer galaxy • 674 views
ADD COMMENTlink modified 2.9 years ago by mshortr0 • written 2.9 years ago by shortridge.150
0
gravatar for Bjoern Gruening
2.9 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

can you explain in more detail what your script would do? A step by step instruction would help us to generate a workflow for you. If you can provide a script we can also help you with integrating this into Galaxy. In the end this is easy :)

Cheers,

Bjoern

ADD COMMENTlink written 2.9 years ago by Bjoern Gruening5.1k
0
gravatar for mshortr
2.9 years ago by
mshortr0
United States
mshortr0 wrote:

Hi there, should this become useful to anyone in the future, here is the tool that I developed for this task:

https://toolshed.g2.bx.psu.edu/view/megan-shortridge/degenerateprimerremoval/33b174991d3e

It can now be downloaded from the ToolShed for Galaxy.

 

Cheers,

Megan

ADD COMMENTlink written 2.9 years ago by mshortr0
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