Re: [Artemis-users] Best way to produce the ACT crunch file?
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 -- -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://publists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Best way to produce the ACT crunch file?
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 -- -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://publists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://publists.sanger.ac.uk/mailman/listinfo/artemis-users
