Hi Alex
Thanks for this. I downloaded your handy nucmer_coords2ACT_galaxy perl
script from the Galaxy server and it works like a charm. Will sure cite it!
Regards
Abhinay
On 17/08/15 15:51, Bossers, Alex wrote:
Abhinay
We use MUMmer to generate those comparison files. Scripts available at our free
public galaxy instance (http://galaxy.wur.nl) can convert those for you to
readable files for ACT. Like WebACT does...
Look in the tool section WUR-tools::MUMmer/Artemis. You may find some more
handy things over there.
Cheers,
Alex
-----Oorspronkelijk bericht-----
Van: artemis-users-boun...@sanger.ac.uk
[mailto:artemis-users-boun...@sanger.ac.uk] Namens Abhinay
Verzonden: woensdag 12 augustus 2015 14:14
Aan: artemis-users@sanger.ac.uk
Onderwerp: [Artemis-users] Best way to produce the ACT crunch file?
Hi
What is the best way to generate a good comparison crunch file for ACT?
The manual is not very helpful. I tried using WebACT but I do not get any output from it.
MSPCrunch also did not work well. tblastx works well but the hits are fragmented. Do you
know of any tblastx parameters that I can tweak to get more "broad" hits. Also,
I want to compare two multi-FASTA files ( indexed by faidx) with associated gff files
(indexed by tabix), so is it possible to create a similar indexed crunch file between
them?
Thanks!
Regards
Abhinay Ramaprasad
PhD Candidate
Pathogen Genomics Laboratory (Dr. Arnab Pain) KAUST
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