trimest tool cuts the begining of my seq names in the output fasta file
Dear galaxy developers, When I use the EMBOSS tool: trimest<https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS%3A%20trimest102/5.0.0>, Trim poly-A tails off EST sequences , within galaxy The sequences names in the fasta output file comes out without their beginning, for instance:
gi|259479195|dbj|AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds Will be shortened into: AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds How can I keep the beginning of the sequence names? Am I doing something wrong? Many thanks for your help Inbar
[Description: logo_50prcnt] Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Building 51, room 323 Email: inbarpl@bgu.ac.il<mailto:inbarpl@bgu.ac.il> Tel: +972-8-6428676 Fax: +972-8-6479035 Web: http://bioinfo.bgu.ac.il<http://bioinfo.bgu.ac.il/>
Hi Inbar If you want to keep the NCBI stile fasta header, you need to change the setting for "Output Sequence File Format:" to "NCBI style FASTA (m)". By default, most EMBOSS tools change the fasta header format to the "EMBOSS" style format. Regards, Hans-Rudolf On 06/16/2013 12:01 PM, Inbar Plaschke wrote:
Dear galaxy developers,
When I use the EMBOSS tool: trimest <https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS%3A%20trimest102/5.0.0>,Trim poly-A tails off EST sequences , within galaxy
The sequences names in the fasta output file comes out without their beginning, for instance:
*gi|259479195|dbj|*AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds
Will be shortened into:
AB491800.1|Brachionusplicatilisstt3mRNAforoligosaccharytransferaseSTT3subunithomolog,partialcds
How can I keep the beginning of the sequence names? Am I doing something wrong?
Many thanks for your help
Inbar
Description: logo_50prcnt
Inbar Plaschkes Bioinformatics Core Facility National Institute for Biotechnology Ben-Gurion University of the Negev Beer-Sheva 84105, Israel
Building 51, room 323 Email: inbarpl@bgu.ac.il <mailto:inbarpl@bgu.ac.il> Tel: +972-8-6428676 Fax: +972-8-6479035 Web: http://bioinfo.bgu.ac.il <http://bioinfo.bgu.ac.il/>
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participants (2)
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Hans-Rudolf Hotz -
Inbar Plaschke