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

Searching Galaxy Tool Shed gives error
by Joachim Jacob 12 Dec '12

12 Dec '12

Hello, Searching the Galaxy toolshed for workflows on http://toolshed.g2.bx.psu.edu/ gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Cheers Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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How to add a built-in index for Tophat2?
by Sachit Adhikari 12 Dec '12

12 Dec '12

TopHat2 needs built-in index/ reference genome in order for it to run. I need to add hg 16 index into the build-in index / reference gnome list. I already have the file. How can I add it? Regards, Sachit

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Galaxy doesn't detect the file when we add dataset to a library under Manage data libraries
by Sachit Adhikari 12 Dec '12

12 Dec '12

Hi list, We have found that, in Galaxy, when we add dataset to a library under Manage data libraries, Galaxy sometimes detects the type of the file and sometimes does not. What I have noticed is that it detects the type of the file when we select "Copy file into Galaxy" under "Copy data into Galaxy?" option and does not detect it when we select "Link to files ..." Is this a known issue? If it is, is there any workaround to solve the issue? Thanks Regards, Sachit

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Sliding window to get average of a seq reads
by shamsher jagat 11 Dec '12

11 Dec '12

I have a bacterial genome which I divided into bins of 5 bp and counted reads in each bin. Now I want to use a sliding window of say 100 bp and count the average. Is there any option in Galaxy that I can do it I have bed file of data. Thanks Kanwar

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Windows function not working
by shamsher jagat 11 Dec '12

11 Dec '12

I have been trying to use Region variation > Make window but every time it returns empty file without any error I have a bed file of custom genome and has used chrXX 1 10 0.23 Any suggestion please. Thanks

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Tophat error.
by Humberto Boncristiani 11 Dec '12

11 Dec '12

Hi Everyone. Somebody knows what this error message means: An error occurred running this job:Settings: Output files: "/tmp/3010855.cyberstar.psu.edu/tmpU4RslD/tmpNmgc_h.*.ebwt" Line rate: 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default Thanks. Humberto.

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Downloading the gene coordinates of the rice genome
by maheshi dassanayake 10 Dec '12

10 Dec '12

Dear Galaxy users, Does anyone know how I can download the gene coordinates for the genome build: oryza_sativa_japonica_nipponbare_IRGSP4.0. Thanks a lot for your help. maheshi

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Trimming and thinning of paired-end reads
by Alicia R. Pérez-Porro 10 Dec '12

10 Dec '12

Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by quality my paired-end Illumina reads. As fas as i know if i want to use FASTX-TOOLKIT i have to treat my data as single-end, trim the adapter of the forward reads first and then proceed with the reverse reads. And same thing for the filtering by quality. Right? - Can i combine forward/reverse reads in a unique file with the FASTQ joiner and then proceed with the trimming of the adapters and the filtering by quality? If i do that, am i going to be able to remove the adapters of both directions reads? Am i going to be able to keep the broken pairs? I was reading that there is another toolkit, NGS QC TOOLKIT that allows you to work with paired-end reads and keep the broken pairs after the trimming and thinning. Did anyone try it? I think that has no galaxy option... Thanks, Alicia. –– Alicia R. Pérez-Porro PhD student Giribet lab Department of Organismic and Evolutionary Biology MCZ labs Harvard University 26 Oxford St, Cambridge MA 02138 phone: +1 617-496-5308 fax: +1 617-495-5667 www.oeb.harvard.edu/faculty/giribet/

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Compute sum per row
by Joachim Jacob 10 Dec '12

10 Dec '12

Hi all, I wonder if there is a method for calculating a metric (e.g. sum) per row (working on a tabular dataset). But, each row contains a different number of values (i.e. some columns are empty). Can I compute this, using Compute? Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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Using -q trimming options in bwa
by Aung-Kyaw Chi 07 Dec '12

07 Dec '12

Hi everybody, Have any of you updated the python/xml wrappers so that bwa will accept a '-q' argument for quality trimming? It would really be helpful for what we are doing. I've looked and I haven't found a wrapper that does this. Any suggestion on finding something like it or better yet if you have the code could you please share it with me. Thanks! Sincerely, Aung Chi

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