galaxy-user June 2013

galaxy-user@lists.galaxyproject.org

31 participants
46 discussions

chimeric reads detection
by Delattre Hadrien 17 Jun '13

17 Jun '13

hello, I am a beginner Galaxy user and I need to perform chimeric sequences detection on single end reads (from metatranscriptomic samples). Do someone know a tool for that? thanks hadrien

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BWA failing to index?
by Joshua Orvis 17 Jun '13

17 Jun '13

I just installed a new instance of Galaxy and bwa_wrappers from the main toolshed. I then uploaded a reference genome along with two FASTQ files in order to run "Map with BWA for Illumina". When I run it, I get this error: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln] 157bp reads: max_diff = 7 [bwa_aln] 190bp reads: max_diff = 8 [bwa_aln] 225bp reads: max_diff = 9 [bwt_restore_bwt] fail to open file '/export/galaxy-dist/database/files/000/dataset_1.dat.bwt'. Abort! Aborted I've used the same tool on other Galaxy instances and it always auto-indexes the reference genome here before continuing. What's going wrong? (I made sure bwa was in the user's PATH that is running run.sh)

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fastq-dump on sra files from NCBI
by Murphy, Theresa 17 Jun '13

17 Jun '13

Is it possible to upload files from the NCBI sra data base, then use fastq-dump from the sra toolit within galaxy? If not, could these tools be added? The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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(no subject)
by Loubna Youssar 17 Jun '13

17 Jun '13

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can galaxy analyze SOLiD XSQ dataset except csfasta/qual data?
by Wang, Daqing 15 Jun '13

15 Jun '13

Hello, I wonder if Galaxy take SOLiD XSQ format data as input for mapping. I know it takes csfasta/qual data. Does anyone try this kind of analysis with SOLiD XSQ format? Any feedback and advice is appreciate it. Thank you! Daqing Wang

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genomic coordinates to Enterz gene ids
by shamsher jagat 15 Jun '13

15 Jun '13

I have a list of around 3000 genomic coordinates of mouse genome and I would iike to extract gene name Enetrz gene ids Is it possible to extract this information in galaxy. Thanks Kanwar

2 1

visualization problems
by Ann Holtz-Morris, M.S. 12 Jun '13

12 Jun '13

Hi, Earlier today I couldn't add a new visualization. I just was working again and now I cannot load the viualizations that I'd previously set to load (BAM from SAV). I get the message Internal Server Error Galaxy was unable to sucessfully complete your request.... GURU MEDITATION: #ff39a25b2b684850ba01c9bdc9eb8942 Thanks for your help! Ann Ann Holtz-Morris SRA III de Jong Laboratory CHORI Oakland Oakland, CA

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another newbie question
by Boaz Shaanan 12 Jun '13

12 Jun '13

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Isochore as Genome coordinates ?
by Abdullah Al Mahmud 12 Jun '13

12 Jun '13

Hi, In my account I have uploaded a file name iso_mm10.bed. The bed files contains coordinates of 6018 isochores of mouse genome mm10. I want to extract GC% of each scores with the list of genes present in each isochores. I tried using extract features, geecee, and many other tools from galaxy. But every time either it said error or no peak. I will be grateful to you if you kindly give me an idea about how to solve this problem. Abdullah -- Abdullah Al Mahmud, PhD Postdoctoral fellow, University of Montreal, Lab. of Dr. Jacques Michaud CHU Sainte-Justine Research Center, Montreal, Quebec, Canada. abdullah.al.mahmud(a)umontreal.ca

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How do I add Ray to Galaxy Central in the tool shed ?
by Sébastien Boisvert 12 Jun '13

12 Jun '13

Hello, I want to add Ray (a scalable de novo assembler for genomes and metagenomes) to Galaxy. Ray is GPLv3 [1]. I have read http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial and I understand that I have to write a Tool Definition File in XML. I also visited the source code here: https://bitbucket.org/galaxy/galaxy-central/src/5de636ce68faededc52d7b0c161… I will also have to write a wrapper for Ray to prepare the command line from the options provided by the Galaxy API. But where is stored the executable (in my case, where is sdtored Ray) ? Does Galaxy include the specs to build all the tools available in Galaxy-Central ? --- [1] http://denovoassembler.sourceforge.net/

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galaxy-user June 2013