On Thursday, August 18, 2011, Jeremy Goecks jeremy.goe...@emory.edu wrote:
I'm picturing select parameter for FASTA output,
Name features using:
* build, reference, co-ordinates and strand (default)
* name from annotation file (if present)
* reference name (useful if working on
On Wed, Aug 17, 2011 at 1:41 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
One idea to address both of these issues is to embed the
original format in the fasta name so that it's clear whether
the coords are BED or GFF (e.g.
hg17_BED_chr1_147962192_147962580).
Or
One idea to address both of these issues is to embed the
original format in the fasta name so that it's clear whether
the coords are BED or GFF (e.g.
hg17_BED_chr1_147962192_147962580).
Or hg17_gtf_chr1_147962192_147962580 etc.
That certainly seems better than the current situation.
On Mon, Aug 15, 2011 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Jeremy,
Things do indeed look much better after your commit last night, thanks:
https://bitbucket.org/galaxy/galaxy-central/changeset/3c7416baa157
On Mon, Aug 15, 2011 at 12:52 AM, Jeremy Goecks
On Mon, Aug 15, 2011 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Jeremy,
Things do indeed look much better after your commit last night, thanks:
https://bitbucket.org/galaxy/galaxy-central/changeset/3c7416baa157
On Mon, Aug 15, 2011 at 12:52 AM, Jeremy Goecks
On Mon, Aug 15, 2011 at 3:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Aug 15, 2011 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Thanks. If I manually set the BED strand to column 5, then the extract tool
can be used with both the original NCBI GFF3 file and the BED
However, the FASTA output uses different names because it embeds
the start/end co-ordindates as is. Thus using GFF3 features, the
sequence name includes _883_2691_ while using BED features the
same sequence has instead _882_2691_ for its name.
I propose this be harmonised by always using
Sorry -more questions - could you explain what the Interpret features
when possible setting in the Extract Genomic DNA is meant to do?
The tool's help text doesn't say anything (other than it is only for
GTF/GFF files).
In the NC_005213.1 example turning Interpret features when possible
on
Great. Could you try that example on the latest galaxy-central please?
I have revision 06f0bca6de24 and get the following error using the
steps given earlier:
Traceback (most recent call last):
File
/home/pjcock/repositories/galaxy-central/tools/extract/extract_genomic_dna.py,
line
I think I've found another problem in exploring possible workarounds,
1. Goto http://usegalaxy.org (or a local Galaxy running galaxy-dist or
galaxy-central)
2. Import this GFF3 file,
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans_Kin4_M_uid58009/NC_005213.gff
3. Click on
Well, sort of. After converting that GFF3 file into BED, the strand column
isn't set in the metadata. That seems important!
We'll look into this.
Also a point of clarification, I had the wrong URL for the FASTA file.
This is the whole genome, although to actually proceed with this
Hi all,
Is this a bug, or have I misunderstood something?
1. Goto http://usegalaxy.org (or a local Galaxy running galaxy-dist)
2. Import this genomic FASTA file,
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Nanoarchaeum_equitans_Kin4_M_uid58009/NC_005213.ffn
3. Import this GFF3 file,
Actual result: Red error against the gff file,
Unspecified genome build, click the pencil icon in the history item to
set the genome build
The fact I'm using a FASTA file from my history should mean the genome
build is irrelevant as that only applies to locally cached genomes
(right?).
On Fri, Aug 12, 2011 at 2:25 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
Actual result: Red error against the gff file,
Unspecified genome build, click the pencil icon in the history item to
set the genome build
The fact I'm using a FASTA file from my history should mean the genome
On Fri, Aug 12, 2011 at 2:45 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Aug 12, 2011 at 2:25 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
Actual result: Red error against the gff file,
Unspecified genome build, click the pencil icon in the history item to
set the genome
On Fri, Aug 12, 2011 at 3:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On the bright side, convert to BED seems to work.
Well, sort of. After converting that GFF3 file into BED, the strand column
isn't set in the metadata. That seems important!
Also a point of clarification, I had the
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