User: David Matthews

gravatar for David Matthews
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630
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United Kingdom
Last seen:
10 months, 3 weeks ago
Joined:
7 years, 5 months ago
Email:
d***********@bristol.ac.uk

Posts by David Matthews

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Tophat Error
... Hi Jen, Many thanks for this, much appreciated. Will give it a try - fingers crossed! David. Sent from my phone, so please excuse my mistakes. To: David Matthews; Galaxy Dev Cc: galaxy-user; Jeremy Goecks Subject: Re: [galaxy-dev] [galaxy-user] Tophat error Hi David, I don't know if you are stil ...
written 6.1 years ago by David Matthews630
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Comment: C: Tophat Error
... Hi, Thanks for the reply, sorry about the multiple posts - it kept getting bounced so I resubmitted the question. We seem to be having real problems with our local install so I'll add it to the list...! Cheers David ...
written 6.1 years ago by David Matthews630
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Tophat Error
... Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue ...
bam samtools bowtie alignment written 6.1 years ago by David Matthews630 • updated 6.1 years ago by Jennifer Hillman Jackson24k
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Tophat Error
... Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tu ...
bam samtools bowtie alignment written 6.1 years ago by David Matthews630
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Tophat Error
... Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue ...
bam samtools bowtie alignment written 6.1 years ago by David Matthews630
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Make A Vcf File
... Hi, This may be a dense question, but how do we generate a vcf file from the public version of Galaxy? Am I missing something obvious? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, ...
galaxy written 6.2 years ago by David Matthews630 • updated 6.2 years ago by Jennifer Hillman Jackson24k
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Answer: A: Bwa Not Recognize Fastq Query File
... Hi, I;m wanting to run BLASTp on the test site to compare it to some test runs here on our local copy but the tool does not run saying "Index file named 'blastdb_p.loc' is required by tool but not available". Is this me doing something wrong or is it something missing at the test site? Best Wishe ...
written 6.3 years ago by David Matthews630
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Answer: A: Suggestions For De Novo Assembly Plant Transcriptome Without Reference
... Hi Jane, I have used Trinity on a local installation here at Bristol University. The main reason its not on Galaxy main is because its very very memory intensive (we run it on nodes with 256GB RAM). So you really need access to a big machine to run it. Having said all that the output is astoundingl ...
written 6.3 years ago by David Matthews630
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Comment: C: Public Interface Issues
... Hi, Sorry to add to the list of problems but I can't see "my history" at all, I can only see the main pane and the list of tools. Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, Schoo ...
written 6.4 years ago by David Matthews630
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Comment: C: Selecting Reads At Random From Fastq File
... Hi, This may be a bit dumb or missing the point but just selecting the first 5 million is kind of random isn't it? I mean where the reads map and what they are from is not known to you and they were not collected by the sequencer in a manner that is influenced by the nature of the sample? Best Wi ...
written 6.5 years ago by David Matthews630

Latest awards to David Matthews

Popular Question 6.1 years ago, created a question with more than 1,000 views. For A Genbank To Gtf Converter
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Calculating Percent Coverage Over The Target Genome
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Downloading Large Files From Galaxy
Popular Question 6.1 years ago, created a question with more than 1,000 views. For P_Ids And Cufflinks

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