not sure about compatibility EnsEMBL gtf files, but differences between the various patches are represented here:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtmlHuman genome reference now at Patch 4 (which was news to me until I went to this page, thx!).
f.
-- B.F. Francis Ouellette http://oicr.on.ca/research/ouellette/
On 2011-06-10, at 8:21 AM, David Matthews wrote:
Dear Galaxy-users,
Does anyone know what the differences are between hg19 and hg19patch2 and can anyone tell me if the latest ensembl gtf file (v62) is definitely compatible with both hg19 and hg19patch2?
Best Wishes, David.
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058 Fax. +44 117 3312091
D.A.Matthews@bristol.ac.ukmailto:D.A.Matthews@bristol.ac.uk
On 10 Jun 2011, at 11:39, Michal Stuglik wrote:
Hi Jen,
It works, thanks!
I am wondering why using Text Manipulation/Compute function, galaxy changes brackets '[' to '__ob__' and '__cb__' for ']', so for this: str(c1)[1:2] --> str(c1)__ob__1:2__cb__
thanks a lot, michal
Hi Michal,
The tool "Fetch Sequences -> Extract Genomic DNA" can be used to extract fasta sequences. The coordinates can be BED, GTF, etc. and the "genome" doesn't necessarily have to be an actual genome, just a fasta file in your history.
To subset a data string, the tool "Text Manipulation -> Trim" might be helpful. This would only work if you want to use the same rules for an entire file (or split your file up and run the tool on those subfiles using different rules). Practical for some cases, but not all.
And the final option is for coordinate data - tools in "Operate on Genomic Intervals". Once you have the final coordinate set, going back and using the "Fetch Sequences" tool can capture the associated result fasta sequence, from a native genome or a fasta file in your history, as described above.
Hopefully this gives you an option that will work for your project,
Best,
Jen Galaxy team
On 6/5/11 7:14 AM, Michal Stuglik wrote:
Hi all,
I am wondering if galaxy has tool to substring/extract sequence/text from another sequence/text based on coordinates in columns (start, end column) or how to do it in Text Manipulation/Compute?
all the best, michal
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