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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