trimest tool cuts the begining of my seq names in the output fasta file

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trimest tool cuts the begining of my seq names in the output fasta file

Inbar Plaschke

Dear galaxy developers,

When I use the EMBOSS tool: trimest, 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: [hidden email]
        Tel: +972-8-6428676
        Fax: +972-8-6479035
        Web: http://bioinfo.bgu.ac.il

 


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Re: trimest tool cuts the begining of my seq names in the output fasta file

Hans-Rudolf Hotz
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: [hidden email] <mailto:[hidden email]>
>          Tel: +972-8-6428676
>          Fax: +972-8-6479035
>          Web: http://bioinfo.bgu.ac.il <http://bioinfo.bgu.ac.il/>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/