Hello Karen,

The following general workflow should help you to pull sequences from any source.


1) cut out the sequence IDs from the query (in this case, a GTF & BED file) and sort them.
Text Manipulation -> Cut columns from a table
Filter and Sort -> Sort
2) convert the target fasta file to tabular format
Convert Formats ->  FASTA-to-Tabular converter
3) join the two datasets based on the sequence ID
Join, Subtract and Group -> Join two Queries
4) covert to fasta
Convert Formats -> Tabular-to-FASTA
5) when starting with a GTF file, there will most likely be duplicates. To remove, use:
NGS: QC and manipulation -> Collapse sequences

Once you create the actual workflow that performs the job, be sure to save it so that you can just re-use it whenever you need to perform the same task. To do this, from the history pane (most right) use Options -> Extract workflow and following the instructions on the form to customize.

Hopefully this helps,

Jen
Galaxy team

On 1/26/11 12:05 PM, Karen Tang wrote:
Hi Galaxy people,

I have transcripts predicted by Cufflinks that are in a gtf file. How
can I extract the sequences corresponding to those transcripts, using
Galaxy?

[Cufflinks transcript predictions in gtf file] + [Genome sequence in
FASTA file] ---> [FASTA file of transcript sequences]

My genome is a custom genome (not at UCSC).

---------

I'll also need to do the same thing, except my predicted transcripts are
in a Scripture bed file.

Thanks for your help!

Karen Tang :)
Plant Biology
University of Minnesota

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Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
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