[galaxy-user] TSS list with annotation for Hg19

2011-06-03 Thread shamsher jagat
I want to extract TSS ids with correspodning location for Hg19. Once I extract such TSS coordinates I want to have there annotation either with enetrz gene id or some other unique Ids. I am sure Galaxy can do this, But I dont know where to start, or which workflow to use. Can some one please dirce

Re: [galaxy-user] suggestion for multithreading

2011-06-03 Thread Louise-Amélie Schmitt
Le 02/06/2011 21:39, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: default_cluster_job_runner will remain for backwards compatibility, but we'll ship a sample job_conf.xml that runs everything locally by default. --nate Haha, and I did that before realizing I could do just what I needed b

Re: [galaxy-user] suggestion for multithreading

2011-06-03 Thread Nate Coraor
Louise-Amélie Schmitt wrote: > Le 02/06/2011 21:39, Nate Coraor a écrit : > >Louise-Amélie Schmitt wrote: > >>>default_cluster_job_runner will remain for backwards compatibility, but > >>>we'll ship a sample job_conf.xml that runs everything locally by > >>>default. > >>> > >>>--nate > >>Haha, and

Re: [galaxy-user] Flagstat crashes in non-linear workflows with TORQUE

2011-06-03 Thread Louise-Amélie Schmitt
Le 06/04/2011 13:57, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone I observed an issue when flagstat is incorporated in a workflow in which the BAM file it works on is also used by another program (generate pileup for instance) and is NOT the input dataset (generated by sam

Re: [galaxy-user] Flagstat crashes in non-linear workflows with TORQUE

2011-06-03 Thread Nate Coraor
Louise-Amélie Schmitt wrote: > Le 06/04/2011 13:57, Nate Coraor a écrit : > >Louise-Amélie Schmitt wrote: > >>Hello everyone > >> > >>I observed an issue when flagstat is incorporated in a workflow in which > >>the BAM file it works on is also used by another program (generate > >>pileup for instan

Re: [galaxy-user] TSS list with annotation for Hg19

2011-06-03 Thread Jennifer Jackson
Hello, One direct method is to import data using "Get Data -> BioMart". Choose "ENSEMBL GENES 62", then "Homo sapiens genes (GRCh37.p3)". In the left side bar, click on "Attributes". In the resulting form, select "Structures", then open GENE and check "Transcript Start" and "Associated Gene N

[galaxy-user] Loading files to local Galaxy

2011-06-03 Thread Tilahun Abebe
Hi guys, We are trying to load Illumina data to our local Galaxy instance. The files are between 700 MB and 2.2 GB. Files below 2 GB load in less than 5 minutes. Files larger than 2 GB don't upload at all. We installed Galaxy locally because we thought loading files will be faster than the se

Re: [galaxy-user] TSS list with annotation for Hg19

2011-06-03 Thread Jennifer Jackson
Short update: I forgot to mention that you will probably want to include the chromosome and strand under the "GENE" options. Also, do not select "Associated Gene DB" during the export (just examine this at BioMart to note the source) as this will output some html content not allowed in a Gal

Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

2011-06-03 Thread Robert Curtis Hendrickson
Jennifer, Thanks for your help so far. I've been trying to implement the approach you outlined. It seems to be taking a lot of steps. I think I'm now at the last step, where I convert my TAB format file into a BED and push it to USCS for viewing. But I don't see anything that will allow me t

Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

2011-06-03 Thread Jennifer Jackson
Hi Curtis, Two more steps were needed, I ran them in this history: http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/re-galaxy-user-ucsc-embossfuzznuc-ucsc-workflow-63 1 - removed the first column ("hg19") from dataset #38, using the "Text Manipulation -> Cut" tool 2 - in the resulting dataset