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Question: Cutadapt with option of using adapter Fasta file
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gravatar for hkhoja
13 months ago by
hkhoja • 0
United States
hkhoja • 0 wrote:

Hi,

The cutadapt tool available in the galaxy tool shed only allows for the manual input of the adapter sequence, or picking an adapter sequence from the drop down menu one at a time controlled by tab delimited text file. Does anyone have access to a modified wrapper that would allow for using an adapter.fasta file for the list of adapters similar to the command line version? I am putting together a workflow using galaxy and this is the only step we have to do manually. Since we have to trim over 150 adapters from our reads in both 5’ and 3’ having the adapter input file option will be extraordinarily helpful. Any help would be greatly appreciated.

Thank you

Hamid
galaxy • 744 views
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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by hkhoja • 0
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gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The only QA tool I know of that permits the entry of multiple user-defined sequences is the Barcode Splitter tool.

This could be proposed as an enhancement for the Cutadapt tool: Open an issue at the code source repo or write to the tool author through the tool shed. Log in (create an account if needed), click the tool name, and use the Repository Action menu in the top right corner. This tool has not been updated in a while, so I am not sure if future development is planned, you'll need to ask. https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/01d94df2e32a

Another option is to see if Trimmomatic using the option to trim known Illumina sequence would work. Maybe give it a try if you haven't already? An enhancement to this tool to allow user-defined sequence is also a possibility, so you could make the same type of request (code repo or through tool shed).

For either, explain your use case and name the tool specifically, including version.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k
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