has anybody an idea how to do the following in galaxy?
I have short (400bp) metagenome reads and I have used meta-Genemark to find
protein coding regions in the unassembled reads. Meta-Genemark outputs a
GFF3 file (you find a sample at the bottom of the post).
I saw that Galaxy has a tool to fetch sequence from a genome file using a
GFF format file: "Extract Genomic
coordinates from assembled/unassembled genomes ". I would like to use
that tool, if possible.
The problem is however that I get the following error: Unspecified genome
build, click the pencil icon in the history item to set the genome build.
Of course I have no genome, so I am a bit stuck and I have no clue on how to
use the coordinates in my GFF file to extract those regions from my
metagenome reads. Anybody an idea for a proper workflow?
##source-version GeneMark.hmm_PROKARYOTIC 2.7d
##date Thu Mar 24 06:15:18 2011
##Sequence file name: ghm.mfa
##Model file name:
FV4B4XA01C8BBF GeneMark.hmm gene 1 513 . + 0 gene_id
FV4B4XA01D6PDN GeneMark.hmm gene 2 334 . + 0 gene_id
FV4B4XA01DC6SS GeneMark.hmm gene 1 390 . - 0 gene_id
FV4B4XA01AOJUF GeneMark.hmm gene 2 400 . - 0 gene_id
FV4B4XA01CMP07 GeneMark.hmm gene 1 465 . + 0 gene_id
FV4B4XA01CIPQZ GeneMark.hmm gene 1 228 . + 0 gene_id
FV4B4XA01DWJZ1 GeneMark.hmm gene 1 459 . - 0 gene_id
FV4B4XA01AUE58 GeneMark.hmm gene 237 488 . + 0
FV4B4XA01C56SJ GeneMark.hmm gene 1 309 . + 0 gene_id
FV4B4XA01C56SJ GeneMark.hmm gene 321 422 . + 0
FV4B4XA01A3DSA GeneMark.hmm gene 3 143 . + 0 gene_id
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: