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On Jun 28, 2013, at 12:01 PM, "galaxy-user-requ...@lists.bx.psu.edu" <galaxy-user-requ...@lists.bx.psu.edu> wrote: > Send galaxy-user mailing list submissions to > galaxy-user@lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-requ...@lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-ow...@lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > HEY! This is important! If you reply to a thread in a digest, please > 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to > the original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread you > are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: gft annotation files (Jennifer Jackson) > 2. Re: Pause function please (Jennifer Jackson) > 3. Problem with ftp server? (Katrien M. Devos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 27 Jun 2013 11:12:38 -0700 > From: Jennifer Jackson <j...@bx.psu.edu> > To: Vijay Kumar <nayaganv...@gmail.com> > Cc: galaxy-u...@bx.psu.edu > Subject: Re: [galaxy-user] gft annotation files > Message-ID: <51cc8096.2030...@bx.psu.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hello, > > The UCSC Table browser can be used to extract a GTF file formatted > dataset. See the tool "Get Data -> UCSC Main". The output format is one > of the choices at the bottom of the tool UCSC form and there is a user > guide below that at the UCSC web site that details how-to for queries. > > Best, > > Jen > Galaxy team > > > On 6/27/13 4:35 AM, Vijay Kumar wrote: >> Dear sir, >> any one suggest me where i download reference annotation gft files for >> zebra finch . i tried ucsc site, but i donot know exact place to get >> gft files. thank u sir.......... >> >> >> ___________________________________________________________ >> 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: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20130627/1d82d862/attachment-0001.html> > > ------------------------------ > > Message: 2 > Date: Thu, 27 Jun 2013 11:30:25 -0700 > From: Jennifer Jackson <j...@bx.psu.edu> > To: "Ann Holtz-Morris, M.S." <aholtzmor...@chori.org> > Cc: "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu> > Subject: Re: [galaxy-user] Pause function please > Message-ID: <51cc84c1.6010...@bx.psu.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Ann, > > A pause function that truly stops an alignment job, permits inspection > of intermediate results, then resumes it, is probably not going to be > implemented. But we'll send more feedback about that if I have it incorrect. > > The best advice I have to consider running a smaller sample of data > through as a test set. It can be tricky to make truly "representative" > test sets at first pass, but after this run completes, you could > probably identify one by coordinates by choosing all of the sequences > that fit within a certain "slices" of genomic regions that contain > transcript models (or whatever feature you are examining) that are > interesting (or difficult!). Then use that with subsequent runs if you > want to tune parameters and have it run quicker. This is what I usually > do - being sure to include some of the uglier regions. Even if I am > never really able to solve them completely, at least I know what they > will look like in the end. You don't want to train your parameters on > all "ideal" cases. With lower quality data, this might be even more > important since you've got a double challenge to manage - query and > target. But that's real data! > > Good luck with your project, > > Jen > Galaxy team > > On 6/26/13 2:33 PM, Ann Holtz-Morris, M.S. wrote: >> >> Hi, >> >> I read >> https://www.google.com/url?q=http://dev.list.galaxyproject.org/Can-t-find-new-pause-resume-functionality-in-Dec-2012-Galaxy-td4657331.html&sa=U&ei=KFzLUaHFCaGcjALSq4GQCw&ved=0CAcQFjAA&client=internal-uds-cse&usg=AFQjCNHSziHrbCCmumvDDUtmAeW9RvLRdg >> with interest. >> >> I would also like a Pause function as a toggle on/off so I can stop >> look at the data being generated. I'm running a BWA alignment that's >> been working now for almost 48 hours. It's a decent sized data set but >> it had a very low quality second sequencing read. I've quality trimmed >> and length filtered. It ended up being only ~50% of the # of reads in >> Read1. >> >> I'd love to be able to pause it and see if the data set is behaving >> as expected. >> >> Thanks, >> >> Ann >> >> Ann Holtz-Morris >> >> SRA III >> >> de Jong Laboratory >> >> 510-428-3885 x 5715 >> >> aholtzmor...@chori.org <mailto:aholtzmor...@chori.org> >> >> Shipping and Mailing Address >> >> Attention: Ann Holtz-Morris >> >> CHORI-BACPAC Resources BLMR Bldg. >> >> 747 52^nd St. >> >> Oakland, CA 94609-1809 >> >> CONFIDENTIALITY NOTICE: This electronic message is intended to be for the >> use only of the named recipient, and may contain information that is >> confidential or privileged. If you are not the intended recipient, you are >> hereby notified that any disclosure, copying, distribution or use of the >> contents of this message is strictly prohibited. If you have received this >> message in error or are not the named recipient, please notify us >> immediately by contacting the sender at the electronic mail address noted >> above, and delete and destroy all copies of this message. Thank you. >> >> >> ___________________________________________________________ >> 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: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20130627/abeab1b9/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Thu, 27 Jun 2013 20:33:35 -0400 > From: "Katrien M. Devos" <kde...@uga.edu> > To: galaxy-u...@bx.psu.edu > Subject: [galaxy-user] Problem with ftp server? > Message-ID: > <CAMU-1xh1gWG9BK5GK0=w3o-hhdntn61qdqr6x+cewzesbbt...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > I successfully uploaded files to the main Galaxy server this morning using > ftp. However, any attempts to upload files since around noon have failed. > I get a 'Could not connect to server' error when trying to connect to > main.g2.bx.psu.edu uisng FileZilla. Any suggestions? > Thank you. > Katrien > > -- > Katrien M. Devos > Dept. of Crop and Soil Sciences & Dept. of Plant Biology > University of Georgia > Athens, GA 30602 > USA > Tel: (706) 542-0925 > Fax: (706) 542-0914 > E-mail: kde...@uga.edu > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20130627/5498f0f3/attachment-0001.html> > > ------------------------------ > > _______________________________________________ > galaxy-user mailing list > galaxy-user@lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > End of galaxy-user Digest, Vol 84, Issue 27 > ******************************************* ___________________________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
