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Prolonged - Job waiting to run
by Veranja Liyanapathirana 12 Apr '13

12 Apr '13

Dear Galaxy team, I am running short read alignments with Bowtie for illumina using some data generated from split data using barcode splitter. The alignment programme has been indicated the "job waiting to run" status for nearly over an hour. I can meanwhile perform other functions such as data uploading and trimming, splitting etc where the job is continued and completed. Thank you, Kind regards, Veranja Veranja Liyanapathirana, Graduate Student, CUHK

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min alignement count
by Davide Degli Esposti 12 Apr '13

12 Apr '13

Dear Galaxy team, I am performing a differential expression analysis with a cufflinks-cuffmerge-cuffdiff workflow. I was wondering if the default value of 10 fragments for min alignment count is intended to exclude from the significance test all the loci under 10 counts across all samples or if the counts are 10 for at least one sample the test is performed? I thank you for your help Best regards davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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problem with GenomeSpace Exporter
by Gema Sanz Santos 12 Apr '13

12 Apr '13

Dear all, I'm trying to send some data from Galaxy to GenomeSpace, so I can work with this data in Cistrome but I always got this error: GURU MEDITATION: #57662f6109d0460791fa7122116f80ce Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. Could you please indicate me what to do? Thank you in advance Regards, Gema

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Internal Server Error and slow to refresh History
by Gene Genome 11 Apr '13

11 Apr '13

Hi All, When I tried to download the filtered datasets from my History at Galaxy to my computer, I always got this error information: "Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #8aa15caba14d4a3e85ce7ab069" What is the cause for this problem? In addition, It takes about 3 to 5 minutes to refresh my Histories or to view different Histories. However, it is very quick to refresh "Saved Histories". Is it normal? Thanks. Best, Jianguang

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raw count of genes
by Els Willems 11 Apr '13

11 Apr '13

Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-informatics field. I performed an RNA-Seq experiment with single end 50 bp reads to find differential gene expressions between different groups. I have mapped this data with Tophat. Does anyone know how I can get the raw data count out of galaxy in a tab-delimited file? I would like to perform a statistical analysis in other software, without the RPKM normalization that cufflinks offers. Thank you very much. Have a nice day. Yours Sincerely, Els --- Ir. Els Willems KU Leuven Department of Biosystems Division Livestock - Nutrition - Quality Laboratory of Livestock Physiology Kasteelpark Arenberg 30 bus 2456 B - 3001 Heverlee T (+32) 016 32 17 29 F (+32) 016 32 19 94

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Are reads of 36nt in length long enough to accutatly map on splicing junctions?
by Du, Jianguang 11 Apr '13

11 Apr '13

Hi All, I have a very basic question. I have RNA-seq datasets of several cell types and want to compare the alternative splicing events between cell types. The reads are 36nt in length. Are these reads long enough to map on the splicing jucntions accurately when I run Tophat with stringent parameters (no mismatch)? Thanks. Best, Jianguang Du

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merging fastq files
by Thompson, Andrew 10 Apr '13

10 Apr '13

Hi I have received Illumina paired-end genome sequence data as a .tar file. When unpacked the data for each genome accession is split into about 100 fastq files. Total of about 37 Gpb per genome. Can you recommend the best way to organise this data prior to mapping to reference genome? I can concatenate unpacked files using DOS command line into forward and reverse before uploading: is this the best approach? Is there a tools that will start with the .tar file? Andrew

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Parameters for merging BAM files
by Du, Jianguang 10 Apr '13

10 Apr '13

Hi All, I want to merge the Tophat output (Accepted Hits) of Several datasets. I want the merged BAM file has the exact format as the individual input BAM files, should I check "Merge all component bam file headers into the merged bam file"? Thanks. Have a nice weekend. Jianguang

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Using segments of sequences as a reference genome - Bowtie for Illumina
by Veranja Liyanapathirana 10 Apr '13

10 Apr '13

Dear all, My problem seems like something that should have a very simple solution from my end and due to my lack of knowledge in bioinformatics, I am probably messing up with the workflows. The experiment I run is one where we used Miseq to sequence amplicons of a multiplex PCR. We introduced an inhouse barcodeto our PCR products via an adaptor. Miseq data was demultiplexed for the Illumina barcodes using Miseq reporter on intrument software by our service provider and I am trying to run the rest of the process on Galaxy web port with no command prompt programming. The data for R1 and R2 was imported, and then I used barcode splitter to de-multiplex the amplicons after quality triming. (I did not use FASTQ groomer as Miseq data is supposed to be Sanger FastQ than Illumina). Then the sequence trimmer was used to trim the barcode+adaptor sequences. The results of this were re-uploaded and designated as FASTQ for alignment. Now for the reference genome, as our aplicons are of from different sequences, we have segmented FASTA sequences in one file with different FASTA identifiers. When this file was input as the reference genome and mapping was performed using Bowtie for Illumina, the mapping went on with no errors. I could filter the alignment file using SAM filters too. But I can not do any more downstream visualozations, not even SAM to BAM conversion. I suspect that this may be due to an error in the way that the reference genome was formulated but can not get around to figure it out. I would be extremely grateful if you could help me with this issue. I tihnk if I string together the sequences as one it would work, but converting this back for interpretation becomes an issue then. Thank you, Kind Regards, Veranja Veranja Liyanapathirana Graduate Student (Microbiology)

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problem using Depth of Coverage (GATK)
by Gema Sanz 09 Apr '13

09 Apr '13

Hello, I´m trying to use depth of coverage to check the coverage of my reads. I already have the bam files (created with sam to bam) but they are still not recognized by depth of coverage and I got this error message: "Sequences are not currently available for the specified build" I used "human (homo sapiens) hg19 full" for mapping but I can´t select it, it only allows b37 version. I tried to change the build in edit parameters to b37 and then it is recognized but I got another error at the end of the analysis. Any suggestions? Thank you very much in advance Gema

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