Help For Trim Sequences

Question: Help For Trim Sequences

5.0 years ago by

Hi, I am a galazy user and I want to trim exact sequences (not the location) from 5' end. Is there any tool I can use for this? For example, *AATGATACGGCGACCACCG **AACACTGCGTTTGCTGGCTTTG*ATG *so I can get "**AACACTGCGTTTGCTGGCTTTG*ATG" only. If I use trim sequences or FASTX trimmer, then it will be trimmed absolute position. It would be great help. Thank you so much! Best, *Seung Hee *

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modified 5.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.0 years ago by Seung Hee Cho • 10

5.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Seung Hee, I know we discussed this on the other list, but I didn't point you to the open development ticket to (potentially) extend the functions of the "Cut" tool. This is not being actively worked on right now, but you can follow it for updates if you want. https://trello.com/c/CbFSHrU5 Others are still welcome to comment about what types of solutions they might have to offer. There is no specific tool to do this on Main right now (or in the Tool Shed, from my checks). http://usegalaxy.org/toolshed Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

This tool of mine might do what Seung Hee wanted, but I have not tried it on very large Illumina datasets: http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip Regards, Peter

ADD REPLY • link written 5.0 years ago by Peter Cock • 1.4k

Thanks Peter for another option! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

You might also use ( / add to main) the CutAdapt tool, which is available in the main toolshed. It takes multiple adapters, allows 3/5/both side adapters, and is fast. http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=User.use rname&operation=view_or_manage_repository&id=f19bc86bac946438 Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

ADD REPLY • link written 5.0 years ago by Geert Vandeweyer • 20

Thanks Geert, This tool was in the back on my mind, but I couldn't find it last week for some reason! Seung Hee - this is a very good choice, for use in a local or or cloud Galaxy. http://getgalaxy.org http://usegalaxy.org/cloud I think I will close out the ticket below and point it to CutAdapt as a solution. A ticket to ask for this tool to be on Main is a distinct subject/issue - if someone wants to submit that request, the community can vote, team can priotitize, etc. http://wiki.galaxyproject.org/Issues The tool Peter mentions can also be examined. One may fit your needs better than the other, Thanks!! Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD REPLY • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

5.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Seung Hee, You can request that this tool be added to the public Main server at usegalaxy.org through Trello and the team will consider it. For right now, the options are local or cloud. (as in my other reply) Or, you can look around the the other public servers hosted by our community - each is run by a distinct group with their own contact/help/public-use criteria: http://wiki.galaxyproject.org/PublicGalaxyServers It may be simplest to see if a local will do the job, then upload the results to the public server for downstream analysis. Just do the very basics of a "production server" install and then add the tool to test it out. This will take some line commands to set up, but shouldn't be too much of an investment. The links are: http://getgalaxy.org http://usegalaxy.org/toolshed http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_an d_uninstalling_tool_shed_repositories_within_a_Galaxy_instance Local install help/discussion: galaxy-dev@bx.psu.edu Subscribe or search prior Q/A: http://wiki.galaxyproject.org/MailingLists Take care, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 5.0 years ago by Jennifer Hillman Jackson ♦ 25k

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