- galaxy-user - lists.galaxyproject.org

Request to Add Reference Genome
by Matthew Biggs 05 Dec '11

05 Dec '11

Hello Galaxy Team, I am writing to request that the genome of *Sinorhizobium meliloti *1021 be added to the "Map with Bowtie for Illumina" tool. I am using the main server http://main.g2.bx.psu.edu/ and my user name is mbiggs. Please let me know if this email is received. Thanks, Matt Biggs

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Define a path for the command files
by Toqa Manasrah 05 Dec '11

05 Dec '11

Hi everybody, I am integrating a new tool which depends on several other libraries (part of the tool). when galaxy run my tool, it can find main command but not the deepest. where should I define the path of the libraries and command folders I need. by teh way, all these commands and libraries are copied inside the tool directory. Thank you,

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there was a wrong link in my previous mail - gtf file issues
by Noa Sher 04 Dec '11

04 Dec '11

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Problem creating GTF file for use with cufflinks
by Noa Sher 04 Dec '11

04 Dec '11

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Galaxy-Announce: A new, moderated, low-volume Galaxy Mailing List
by Dave Clements 02 Dec '11

02 Dec '11

Hello all, There is a new mailing list in the Galaxy: Galaxy-Announce. Galaxy-Announce is a *moderated, low-volume *mailing list. Galaxy-Announce complements the existing Galaxy-User (about the public server at UseGalaxy.org) and Galaxy-Dev (deployment and development) mailing lists. However, unlike those relatively high-volume mailing lists, Galaxy-Announce will only have a few messages each month. If you are looking for a Galaxy list that just covers the big stuff, this is your list. To subscribe to the list please add your email address to the list here: http://lists.bx.psu.edu/listinfo/galaxy-announce See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Chip-seq data
by Giuseppe Petrosino 30 Nov '11

30 Nov '11

Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSSSSSUSSTTTUTSSSSSSSSSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSTTTTSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGAAAAGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTVVVVUVVWVVUVVUWVVVWWWWWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe

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mapping tags
by Soetkin Versteyhe 30 Nov '11

30 Nov '11

Dear all, I would like to map (e.g. with Bowtie) collapsed sequences (tags) instead of individual sequence reads. Does anyone know if this is possible in Galaxy? Thank you in advance. Best regards, Soetkin Versteyhe, PhD PostDoc University of Copenhagen Faculty of Health Sciences The Novo Nordisk Foundation Center for Basic Metabolic Research Integrative Physiology Blegdamsvej 3B 2200 København N Denmark PHONE +45 35337116 soetkin.versteyhe(a)sund.ku.dk http://sund.ku.dk http://metabol.ku.dk<http://metabol.ku.dk/> [cid:image001.gif@01CCA385.44DE02C0]

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Patch for better FASTQ description handling
by Florent Angly 30 Nov '11

30 Nov '11

Hi, I have found some issue with the way FASTQ read description is handled by Galaxy utilities: https://bitbucket.org/galaxy/galaxy-central/issue/665/paired-end-code-misha… Please consider pulling my patch, thanks, Florent

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Postdoctoral opening in College Park
by Charles Delwiche 29 Nov '11

29 Nov '11

I have a postdoc opening in my lab that could be an excellent opportunity for members of this list. The project is extremely cool, and will incorporate elements of ecology and systems biology. The position is open now, and I would like to fill it ASAP. Charles Delwiche Genomic basis of species diversity and ecosystem functioning We seek a postdoctoral scholar to collaborate on a project funded by the U.S. National Science Foundation to study the evolutionary basis of species diversity and ecosystem functioning in freshwater green algae. The successful candidate will take intellectual lead on the genomics portion of laboratory and field experiments that will (1) determine how much genetic differentiation is required for species to stably coexist, and (2) determine how mechanisms that allow for coexistence also impact community-level processes such as primary production. The candidate will also pursue his or her own research interests within the broader context of the grant proposal. The candidate will work in Dr. Charles Delwiche's lab at the University of Maryland – College Park, and will collaborate with researchers in the labs of Drs. Bradley Cardinale (an ecologist at the University of Michigan) and Todd Oakley (a phylogeneticist at UC-Santa Barbara). The position requires a Ph.D. in the biological sciences, bioinformatics, or a related field. Experience with high-throughput sequencing, sequence analysis, algal/plant biodiversity, or RNA biology are desirable. This is a three-year position, with the initial appointment being for one year and renewals contingent on successful progress in research. The starting salary will be $ 42,000 with full benefits. The University of Maryland is located in College Park, a suburb of the Washington, D.C. Metropolitan Area, and provides a vibrant cultural and academic environment with easy access to a vast array of Federal research facilities. The position is available immediately. To apply formally, send a curriculum vitae, the names of 3 references, and a brief statement of how your research goals fit with research on algal biodiversity, systematics, and evolutionary biology to: aaalgeee(a)gmail.com -- Charles F. Delwiche Professor, Cell Biology and Molecular Genetics CBMG , 0101J Biosciences Research University of Maryland Building #413 College Park, MD 20742-4407 http://www.life.umd.edu/labs/delwiche tel: 301-405-8286 fax: 301-314-1248 There is still only you, listening to the music of the wind and lost in the stagnant cries of the miseries lost in the eyes of others laughing at you. How can someone so different be so much the same? - Liu Sola

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Re: [galaxy-user] Unable to run SICER or Find Peaks
by Daniel Blankenberg 29 Nov '11

29 Nov '11

Hi AP, Please keep all replies on list, this will allow the community to assist and benefit from these correspondences. SICER requires BED input. To go from BAM to BED: 1.) Convert BAM to SAM 2.) Convert SAM to Interval (Convert SAM to interval) 3.) Convert interval to BED(6+). This can be done by implicitly (by selecting the Interval dataset, which will be marked with '(as bed)' in the SICER input box) or by clicking on the pencil icon and explicitly converting uder the section "Convert to new format". Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Nov 29, 2011, at 1:23 PM, Anupam Paliwal wrote: > Hi Daniel, > > Thanks for your kind attention and advice. > > I have followed the following workflow: I aligned my query sequences to > the reference genome using Bowtie; the Bowtie aligned SAM file was > subjected to filter-SAM before converting it to BAM. I have re-BAM-to-SAM > converted the BAM-file before subjecting it to pileup. > > However, now I do have the Input format file (after pileup of SAM) but am > unable to convert it to BAM format to be able to submit it ti SICER. > > > Please see if you can suggest how to convert the Input files back to BAM. > I have tried changing directly through edit-attributes, but it shows > error. > > AP > > > >> Hi AP, >> >> SICER requires BED formatted input with at least 6 columns (for strand >> information). You can convert your BAM files into SAM and then into >> interval and BED format. Once you have your input in the BED (6+) format, >> you should be able to use these tools. Please let us know if we can >> provide additional information. >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >> >> On Nov 23, 2011, at 12:26 PM, Anupam Paliwal wrote: >> >>> Hi, >>> >>> I want to use SICER or Find Peaks for peak calling on GALAXY. >>> >>> I am using my aligned ChIP-seq tag .BAM files. However for both the >>> tools >>> the history is unable to pick the Bowtie-ligned SAM to BAM converted >>> files. >>> >>> On the other hand, using MACS the same files are working nicely for peak >>> calling. >>> >>> Thanks, >>> >>> AP >>> >>> ___________________________________________________________ >>> 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/ >> >> >

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