August 2012 - galaxy-user - lists.galaxyproject.org

Extracting all CpG-SNPs from dbSNP135
by Richard Henriksson 10 Aug '12

10 Aug '12

Dear Sir / Madam, I'm new to Galaxy. Is there any way to extract all CpG-SNPs from dbSNP135 using Galaxy (preferably as a BED file, but a text file will do)? I tried to figure out myself, but came up short... All help is much appreciated! Sincerely, RH

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how to split paired-end dataset of FASTQ format
by Du, Jianguang 09 Aug '12

09 Aug '12

I downloaded RNA-seq dataset at FASTQ format from SRA of NCBI. I uploaded the dataset onto Galaxy. The dataset is paired-end. I want to split it into two datasets (one for each end) with FASTQ splitter. But the name of the dataset does not appear under "FASTQ reads". How should I do to solve this problem? Thanks. Jianguang

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Streptococcus suis genome
by Joerg Willenborg 09 Aug '12

09 Aug '12

Dear Sir or Madam, with interest I followed up your Galaxy platform and I am planing a Bowtie mapping with RNA-Seq data. Unfortunately the reference genome I am looking for is not included in the drop down menu. Do you think it is possible to add the Streptococcus suis P1/7 (NC_012925.1) genome to the menu? I would appreciate any reply on this email and thank you very much in advance Kind regards Jörg Willenborg Joerg Willenborg, PhD Institute of Microbiology University of Veterinary Medicine Hannover Bischofsholer Damm 15 D-30173 Hannover Germany Tel: +49511-8567595 e-mail: joerg.willenborg(a)tiho-hannover.de

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help for alternative splicing with RNA-seq analysis
by Du, Jianguang 09 Aug '12

09 Aug '12

I have RNA-seq datasets of several cell types. I want to compare alternative splicing events between diffrent cell types. Can anyone show me the protocol/workflow or direct me to the tutorial? Thanks. Jianguang

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downloading a reference genome: Saccharomyces_cerevisiae_S288C_SGD2010
by Douda Bensasson 09 Aug '12

09 Aug '12

We have mapped our ABI SOLiD reads to the "Yeast (Saccharomyces cerevisiae) str. S288C: Saccharomyces_cerevisiae_S288C_SGD2010" reference in Galaxy, and need to compare our yeast genomes to the reference. We have tried to download the only S. cerevisiae S288c genome release listed at SGD for 2010 among their genome releases (http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S…) but this does not align with the consensus sequences generated by mapping against Galaxy's "Saccharomyces_cerevisiae_S288C_SGD2010". Is Galaxy's Saccharomyces_cerevisiae_S288C_SGD2010 reference available for download from Galaxy or from the Saccharomyces Genome Database (SGD)? Best wishes, Douda

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Bowtie mapping waiting to run for 3 days
by Yanina Bogliotti 08 Aug '12

08 Aug '12

Hi, I was wondering if I have to re-run them or if I just need to wait. Thanks, Yanina

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FTP down?
by John Clayton 08 Aug '12

08 Aug '12

Dear Sir or Madam, My recent jobs submiteed to the Galaxy server mapping short reads using the LastZ tool do not start processing. They remain grey after I hit execute and remain indefinitely in the queue even while I am able to start additional jobs subsequently. Do you have any idea what is going on here? I used LastZ before and it worked fine. Many thanks, John -- John R. Clayton, PhD Université de Strasbourg Anopheles Group, CNRS UPR-9022 "Réponse Immunitaire et Développement chez les Insectes" Institut de Biologie Moléculaire et Cellulaire (IBMC) 15, rue René Descartes F-67084 CEDEX Strasbourg France Tel: +33 3.88.41.70.96 Fax: +33 3.88.60.69.22 Email: j.clayton(a)ibmc-cnrs.unistra.fr http://www-ibmc.u-strasbg.fr/ridi/index.php?cont_id=9&lang=en

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rescuing files from local installation of Galaxy
by Amit Pande 08 Aug '12

08 Aug '12

Dear Galaxy, I encountered a problem when downloading my dataset ( 452 GB) from Galaxy as the local installation crashed . How can I retrieve my results for the experiments ? Could you kindly tell me where are such processed files kept in the installed folder locally ? warm regards, Amit

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Can I call SNPs and Indels in Galaxy
by Mathew Bunj 07 Aug '12

07 Aug '12

I have two DNA seq files for hg18 and want identify SNPs in each file as compare dto existing database and also want to find differences (seq variations) among two samples. I was wondering if I can do that or not in Galaxy (public server)? I know I can use liftover to convert into hg19 if need be. Thanks

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Question about SICER out put
by shamsher jagat 07 Aug '12

07 Aug '12

I used SICR to call peaks and have following out put files: 1. test.1removed bed 2. control1 removed .bed 3. test w 200 graph 4. test w200 normalized graph 5. test w200-G600 FDR.05 island.bed 6. test w200-G600 FDR .05 island filtered.bed 7. test w200-G600 FDR .05 island filtered normalized.wig 8. test w200-G600 FDR.05 score island 9. test w200-G600 summary island Which of these files should be used. I think file 5 and 6 are the ones for visualization as well for annotating with genomic regions. I have read the original paper but it is not very clear what these out puts mean. Could some one please guide me what these files mean and what is useful and rest are intermediate files. My second question is authors of SICER has emphasized about teh importance of choosing gap size and window size. gap size they mention 1-3 -5 depending upon the peak distribution, but I see in Galaxy the default is 600 gap size do we need to change it to 1,2- 5 or I am missing something. Any advise please but I did my searching on net. Thanks

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