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] 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
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] 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] 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] 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] 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

Re: [galaxy-user] Extract Genomic DNA Problem

2011-06-21 Thread Jennifer Jackson
paths/files in AlignSec.loc? This is for our local instance of Galaxy. -John 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: Tuesday, June 21, 2011 10:23 AM

Re: [galaxy-user] Displaying MACS Peaks at UCSC

2011-06-21 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] GenBank Submission - How to Generate Fasta (not fastq) files

2011-06-21 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] newbies

2011-06-22 Thread Jennifer Jackson
not sure if this is the right forum. but i need as much access to start up information on the system for developers. we are part of a group in Kenya trying to come up with some apps on a gnome sequencing project we are starting here. regards -- Jennifer Jackson http://usegalaxy.org/ http

Re: [galaxy-user] Chip-Seq, Encode Peaks and Galaxy

2011-06-22 Thread Jennifer Jackson
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] newbies

2011-06-22 Thread Jennifer Jackson
Associate Center for Clinical and Translational Science University of Alabama at Birmingham -- 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] Error running cufflinks on Galaxy

2011-06-22 Thread Jennifer Jackson
[mailto:galaxy-user- boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: Friday, June 10, 2011 3:58 PM To: David Robinson Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Error running cufflinks on Galaxy Hello David, Cufflinks requires locally cached data to perform the Bias

[galaxy-user] June 23, 2011 Galaxy Development News Brief

2011-06-23 Thread Jennifer Jackson
June 23, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/Features/DevNewsBrief/2011_06_23 == Source Distribution == http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 720455407d1c == GCC 2011 == We had ~

[galaxy-user] Error running cufflinks on Galaxy

2011-06-24 Thread Jennifer Jackson
Dear all, I tried to follow the Cufflinks tutorial created by Jeremy. The problems start with first visualization step. The is no overlapping at all between Cufflinks transcripts and RefSeq Chr19 reference, provided on the tutorial page. Was that the goal, or transcripts should overlap and

Re: [galaxy-user] Yeast Genome Assembly

2011-06-27 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] question on cufflinks output

2011-06-27 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] SIFT analysis input and output file

2011-06-28 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] AXT and NIB files for AlignSeq.loc

2011-06-28 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

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