Re: [galaxy-user] query related to lift over

2011-01-03 Thread Jennifer Jackson
of those genes for Rat Nov. 2004 (Baylor 3.4/rn4) Assembly. So how I can do this using lift-over ??? Or is there any other method to do this work ??? Thanks in advance Vaibhav Jain Research Scholar @IGIB Delhi, INDIA -- Jennifer Jackson http://usegalaxy.org

Re: [galaxy-user] Advanced text manipulations in Galaxy

2011-01-03 Thread Jennifer Jackson
___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Re: [galaxy-user] slow ftp uploads

2011-01-05 Thread Jennifer Jackson
, using ftp from our server or from Fetch. Since these are 3Gbyte files, this will take a day to upload. Any suggestions? -- Jennifer Jackson http://usegalaxy.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo

Re: [galaxy-user] MACS follow up

2011-01-10 Thread Jennifer Jackson
? ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy

Re: [galaxy-user] How do i view the version of Galaxy

2011-01-10 Thread Jennifer Jackson
mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Re: [galaxy-user] How to get coordinate information

2011-01-11 Thread Jennifer Jackson
have list of such Id's obtained from ENSRNOG000 and I want to get the information of the transcription coordinates. So how can I get in Galaxy or can I get it directly from UCSC ??? Vaibhav Jain Research Scholar @IGIB Delhi, INDIA -- Jennifer Jackson http://usegalaxy.org

Re: [galaxy-user] Run tools/Workflow from command line

2011-01-19 Thread Jennifer Jackson
to contribute and API wrapper. Thanks, James ___ galaxy-user mailing list [hidden email] http://lists.bx.psu.edu/listinfo/galaxy-use -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, January 14, 2011 9:23 PM

Re: [galaxy-user] Galaxy--upload data file

2011-01-19 Thread Jennifer Jackson
___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Re: [galaxy-user] Gene Name in Cufflink/compare/diff

2011-01-24 Thread Jennifer Jackson
/galaxy-user J. ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ galaxy-user

Re: [galaxy-user] Unsubscribe

2011-01-24 Thread Jennifer Jackson
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user

Re: [galaxy-user] How insert gene IDs?

2011-01-25 Thread Jennifer Jackson
/6682d97aabcbfc0d3b720c1e020e8c644d 76e27d -- Fin del mensaje reenviado ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]

2011-01-28 Thread Jennifer Jackson
Original Message Subject: Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file] Date: Thu, 27 Jan 2011 17:23:11 -0700 From: Brian Foley PhD b...@lanl.gov To: Jennifer Jackson j...@bx.psu.edu Dear Jen, I am not much of a Galaxy user yet, but a long

Re: [galaxy-user] Welcome to the galaxy-user mailing list

2011-02-07 Thread Jennifer Jackson
the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org

[galaxy-user] Stitch MAF help

2011-02-07 Thread Jennifer Jackson
was suggested from galaxy's site to go to https://bitbucket.org/james_taylor/bx-python/wiki/Home I downloaded and installed the bx-python package, but know I dont know which script to run I would appreciate any help Thanks Anna -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] About NCBI refSeq id

2011-02-07 Thread Jennifer Jackson
But this refGene.txt contains only 28108 id's.. It will be a great help that if you can help me to get the chromosome start position of these genes. Thanks, Shibu -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ galaxy-user mailing list galaxy

Re: [galaxy-user] Using the public server for analysis

2011-02-07 Thread Jennifer Jackson
. ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu

Re: [galaxy-user] Generating pileup for SNP analysis

2011-02-16 Thread Jennifer Jackson
your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis

Re: [galaxy-user] Which tools can a file be used with?

2011-02-16 Thread Jennifer Jackson
subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

[galaxy-user] February 18, 2011 Galaxy Development News Brief

2011-02-18 Thread Jennifer Jackson
February 18, 2011 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_02_18 Get Galaxy! http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u

Re: [galaxy-user] galaxy fetch sequences question

2011-02-21 Thread Jennifer Jackson
Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server

Re: [galaxy-user] Text Manipulation

2011-02-21 Thread Jennifer Jackson
To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy

Re: [galaxy-user] Generating pileup for SNP analysis

2011-02-22 Thread Jennifer Jackson
. Hopefully this helps when you do the re-run of the analysis, but please let us know if we can help more. I'll send you a link off-line to a history with some more specific information to your project, Thanks, Jen Galaxy team On Wed, Feb 16, 2011 at 9:10 AM, Jennifer Jackson j...@bx.psu.edu

Re: [galaxy-user] Generating pileup for SNP analysis

2011-02-22 Thread Jennifer Jackson
To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion

Re: [galaxy-user] fastx_clipper.xml and FASTQ Illumina 1.3+?

2011-02-22 Thread Jennifer Jackson
,fastqsanger name=input type=data label=Library to clip / Peter ___ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

[galaxy-user] Fwd: normalizing for number of tags

2011-02-22 Thread Jennifer Jackson
Hi Nadege, I am forwarding your question to galaxy-u...@bx.psu.edu which is the best place to send data questions, so that the entire team can provide input. We will get back to you as soon as possible. Thanks! Jen Galaxy team --- Hi Jen, I am completely new to the field of ChIP-seq and

Re: [galaxy-user] Importing GTF into Galaxy

2011-02-23 Thread Jennifer Jackson
://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy

Re: [galaxy-user] Lost history!

2011-02-23 Thread Jennifer Jackson
are all gone. Any idea what happened? Thank you. Haiping -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org

Re: [galaxy-user] GeneTrack Server Error

2011-02-23 Thread Jennifer Jackson
://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy

Re: [galaxy-user] Problems using aaChanges tool

2011-03-01 Thread Jennifer Jackson
the file. Any one has any suggestion please. I am running Galaxy on local server. Thanks. -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features

Re: [galaxy-user] Join and Sort in Galaxy

2011-03-04 Thread Jennifer Jackson
subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis

Re: [galaxy-user] upload large data set

2011-03-04 Thread Jennifer Jackson
, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server

Re: [galaxy-user] Map with Bowtie job is waiting to run for more than 1 hour...

2011-03-04 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http

Re: [galaxy-user] Fwd: Need a generous help regarding uploading

2011-03-07 Thread Jennifer Jackson
in this regard will be apprceiated. Vasu --- On *Mon, 1/3/11, Jennifer Jackson /j...@bx.psu.edu/* wrote: From: Jennifer Jackson j...@bx.psu.edu Subject: Re: [galaxy-user] Fwd: Need a generous help regarding uploading To: vasu punj pu...@yahoo.com Cc: galaxy-u...@bx.psu.edu galaxy-u

Re: [galaxy-user] Adding the Hydra genome to Galaxy

2011-03-07 Thread Jennifer Jackson
School of Medicine University of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: reste...@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 2/15/11 6:17 AM, Jennifer Jackson wrote: Hello Rob, This genome is being worked on right now

Re: [galaxy-user] Adding the Hydra genome to Galaxy

2011-03-07 Thread Jennifer Jackson
of California, Irvine Irvine, CA 92697-1700 phone: 949-824-7341 e-mail: reste...@uci.edu fax: 949-824-2688 web: http://polyp.biochem.uci.edu/wiki/index.php/Main_Page On 3/7/11 1:12 PM, Jennifer Jackson wrote: Hi Rob, The project ABRM links to several thousand individual WGS submissions

Re: [galaxy-user] Cleaning of fastq files

2011-03-08 Thread Jennifer Jackson
subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis

Re: [galaxy-user] Problem Adding a Custom Build in Trackster

2011-03-08 Thread Jennifer Jackson
/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used

Re: [galaxy-user] Fwd: Question about FTP

2011-03-10 Thread Jennifer Jackson
://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] Problems with the Groomer

2011-03-10 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Cleaning of fastq files

2011-03-10 Thread Jennifer Jackson
, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used

Re: [galaxy-user] CpG Masking changing alignment length?

2011-03-18 Thread Jennifer Jackson
://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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User

Re: [galaxy-user] CpG Masking changing alignment length?

2011-03-18 Thread Jennifer Jackson
Apologies Michael, wrong answer to the wrong question! Please ignore and thanks for the heads up! jen On 3/18/11 10:22 AM, Jennifer Jackson wrote: Hello Daniel, Currently this is not possible through the Galaxy UI, but is is an excellent functionality suggestion that our team has been

Re: [galaxy-user] fastq / nucleotides distribution graph

2011-03-22 Thread Jennifer Jackson
/fastq_nucleotides_distribution_1.png Is there a way to produce a line graph in http://main.g2.bx.psu.edu/ ? Cheers Christophe -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion

Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y

2011-03-23 Thread Jennifer Jackson
://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] A genbank to gtf converter

2011-03-23 Thread Jennifer Jackson
://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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy

Re: [galaxy-user] Tophat version

2011-03-23 Thread Jennifer Jackson
the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server

Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Jennifer Jackson
subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy

Re: [galaxy-user] Convert SOLiD data

2011-03-28 Thread Jennifer Jackson
mapping tool at Galaxy) to Wiggle or Bigwig formats. I would be thankful for the answers and comments. Falak From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson [j...@bx.psu.edu] Sent: Monday

Re: [galaxy-user] galaxy-user Digest, Vol 57, Issue 26

2011-03-28 Thread Jennifer Jackson
: biomart plugin (Greg Von Kuster) 3. Re: Convert SOLiD data (Ryan Golhar) 4. Re: Convert SOLiD data (Jennifer Jackson) 5. Re: Sort index SAM-files automatically (Ryan Golhar) -- Message: 1 Date: Mon, 28 Mar 2011 11:35:15

Re: [galaxy-user] Problems using aaChanges tool

2011-03-28 Thread Jennifer Jackson
, Evan Schwab wrote: Hi Jen, The aaChanges tool is still not supporting the zebrafish Zv9 build. Can you please fix this so that I am able to use the aaChanges tool. It's very important. Thanks Evan -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Pseudo Autosomal regions in Chrs X and Y

2011-03-28 Thread Jennifer Jackson
, at 14:19, Jennifer Jackson wrote: Hi David, Right now we don't have anything built-in to filter out this type of duplication automatically. As a potential option, did you know that we offer a Canonical Female build for certain genomes? This may help with some of the duplication issues

Re: [galaxy-user] labeling sections of the history

2011-03-30 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http

Re: [galaxy-user] aaChanges / BED-to-Codon

2011-03-30 Thread Jennifer Jackson
/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] Recall: Upload file size and user authorization

2011-04-05 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Flagstat on BAM files

2011-04-05 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] One question about the genome coordinates when using Fetch Sequences

2011-04-07 Thread Jennifer Jackson
: 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] BED to GFF

2011-04-07 Thread Jennifer Jackson
, 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] BED to GFF

2011-04-07 Thread Jennifer Jackson
to HG18 for each entry and then see what was there. Does the feature information need to be in the BED file in order for it to get into the GFF file? If so, do you know of a way to map each aligned read to a certain feature? On Thu, Apr 7, 2011 at 2:16 PM, Jennifer Jackson j...@bx.psu.edu mailto:j

Re: [galaxy-user] too many list digests

2011-04-08 Thread Jennifer Jackson
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features

Re: [galaxy-user] Map with Bowtie

2011-04-18 Thread Jennifer Jackson
. 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/ -- Jennifer Jackson http

Re: [galaxy-user] Map with Bowtie

2011-04-18 Thread Jennifer Jackson
in your history. Thanks! Jen Galaxy team On 4/18/11 11:04 AM, Jennifer Jackson wrote: Hello Falak, The tools in Text Manipulation, Filter and Sort, and Join, Subtract and Group are designed to help with this type of file analysis (basic stats). Please explore and let us know if you need help

Re: [galaxy-user] how to generate consensus sequence in galaxy

2011-04-18 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org

Re: [galaxy-user] Suppress reporting hit number

2011-04-20 Thread Jennifer Jackson
, 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] ce6/WS190 bowtie index

2011-04-20 Thread Jennifer Jackson
lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] Reference genome question, arabidopsis

2011-04-20 Thread Jennifer Jackson
genome to be too small (in terms of width in particular). I have to view and scroll through a lot of two or three line entries but if the width was larger then it would be possible to see more entries at one time. -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] ce6/WS190 bowtie index

2011-04-20 Thread Jennifer Jackson
Hello - Few more links that may be helpful: http://bitbucket.org/galaxy/galaxy-central/wiki/DataTables https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies Thanks! Jen On 4/20/11 1:49 PM, Jennifer Jackson wrote: Hello Giovanni, Galaxy does not (yet) support genome downloads

Re: [galaxy-user] SAM to BAM conversion problem

2011-04-21 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Mapping to only 3 genes / targeted resequencing / SOLiD4 / short reads

2011-04-25 Thread Jennifer Jackson
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] importing histories from main

2011-04-25 Thread Jennifer Jackson
lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] getting started with galaxy

2011-04-28 Thread Jennifer Jackson
. 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/ -- Jennifer Jackson

Re: [galaxy-user] Move data between histories?

2011-04-28 Thread Jennifer Jackson
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features

Re: [galaxy-user] uploading files from remote server

2011-05-02 Thread Jennifer Jackson
/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] SNPs, Indels and so on in virus genomes

2011-05-03 Thread Jennifer Jackson
/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] quality stat.

2011-05-03 Thread Jennifer Jackson
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] RNA seq analysis

2011-05-03 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Indel work flow questions

2011-05-03 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Read count issue with clipper/collapser

2011-05-06 Thread Jennifer Jackson
at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please

Re: [galaxy-user] Stastistics _q valu

2011-05-12 Thread Jennifer Jackson
/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should

Re: [galaxy-user] SNP annotation

2011-05-12 Thread Jennifer Jackson
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] Phylogenetic tree viewer ?

2011-05-16 Thread Jennifer Jackson
at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] finding Conserved non coding region

2011-05-16 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] Calling SNP's

2011-05-16 Thread Jennifer Jackson
the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org

Re: [galaxy-user] Calling SNP's

2011-05-16 Thread Jennifer Jackson
team can contribute to replies. This would be especially helpful when you have a new question. On 5/16/11 11:53 AM, sukeerthi teja Rallapalli wrote: Jen, Thank you so much. In the NGS toolbox what option should i choose. Regards Teja -- Jennifer Jackson http://usegalaxy.org http

Re: [galaxy-user] How to Download large files from Galaxy Server?

2011-05-16 Thread Jennifer Jackson
To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion

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

2011-05-16 Thread Jennifer Jackson
/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used

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

2011-05-17 Thread Jennifer Jackson
output. Failing that, is there an easy text manipulation that would convert that fasta header space to a |? Regards, Curtis -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Monday, May 16, 2011 6:50 PM To: Robert Curtis Hendrickson Cc: 'galaxy-user@lists.bx.psu.edu

[galaxy-user] May 20, 2011 Galaxy Development News Brief

2011-05-20 Thread Jennifer Jackson
May 20, 2011 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_05_20 Prior releases: https:bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs 2011_04_08 Highlights Picard FastQC NBIC Galaxy Hackathon Results

Re: [galaxy-user] biomart error

2011-05-31 Thread Jennifer Jackson
/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should

Re: [galaxy-user] Concatenate fasta tool problem

2011-05-31 Thread Jennifer Jackson
lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

Re: [galaxy-user] error occurred when converting the SOLID output to fastq

2011-05-31 Thread Jennifer Jackson
://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] Mycoplasma pneumoniae M129 and FH reference genome

2011-05-31 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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

2011-06-03 Thread Jennifer Jackson
Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Wednesday, May 18, 2011 11:45 AM To: Robert Curtis Hendrickson Cc: galaxy-user Subject: Re: [galaxy-user] UCSC-EMBOSS/fuzznuc-UCSC workflow? Hello Curtis, The BED extraction data can be resolved in Galaxy. Pull out the whole gene

Re: [galaxy-user] substring sequence on coordinate in columns

2011-06-08 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Re: [galaxy-user] extract alignment for a set of genes

2011-06-10 Thread Jennifer Jackson
, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server

Re: [galaxy-user] Error running cufflinks on Galaxy

2011-06-10 Thread Jennifer Jackson
://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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

Re: [galaxy-user] SAM to bigbed

2011-06-13 Thread Jennifer Jackson
to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] can I merge histories?

2011-06-14 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org

Re: [galaxy-user] MACS

2011-06-14 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org/ http

Re: [galaxy-user] working collaboratively in a history: How To?

2011-06-14 Thread Jennifer Jackson
: https://bitbucket.org/galaxy/galaxy-central/wiki/Home Thanks for using Galaxy! Jen -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other

Re: [galaxy-user] Extract Genomic DNA Problem

2011-06-21 Thread Jennifer Jackson
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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org

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