User: Guy Reeves

gravatar for Guy Reeves
Guy Reeves770
Reputation:
770
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Trusted
Location:
Germany
Last seen:
1 week, 1 day ago
Joined:
2 years, 3 months ago
Email:
r*****@evolbio.mpg.de

Posts by Guy Reeves

<prev • 190 results • page 1 of 19 • next >
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Answer: A: GATK Select Variants Reference Genome
... HI supinderkr While almost all GATK tools are more trouble than they are worth in galaxy. I do find the 'select variants' tool to be useful and it works fine for me. I am sure that if you make your ref sequence compatible for galaxy (or get an FTP file from some source) and it matches exactly th ...
written 8 days ago by Guy Reeves770
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Answer: A: How to filter SNP and Indel data
... Bowtie outputs a list of potential variants ( a mixture of sites with low quality evidence for a true variant and those with high quality evidence). You now need to use a program to call variants freebayes and mpileup are common and avalible on usegalaxy.org. They can asses information from multipl ...
written 16 days ago by Guy Reeves770
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Answer: A: Making a Pedigree file
... There is no tool for this you will need to create it in a text editor outside galaxy and then upload it. It is a simple tabular format described in http://www.shapeit.fr/pages/m02_formats/pedmap.html I think the first 5 columns are obligatory but the rest are not. It kind of depends what you want t ...
written 18 days ago by Guy Reeves770
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Answer: A: Making a Pedigree file
... There is no tool for this you will need to create it in a text editor outside galaxy and then upload it. It is a simple tabular format described in http://www.shapeit.fr/pages/m02_formats/pedmap.html I think the first 5 columns are obligatory but the rest are not. It kind of depends what you want t ...
written 18 days ago by Guy Reeves770
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Comment: C: How to check unaligned reads?
... HI I can follow what you have done. However it is a little unclear what biological question you are trying to answer so it is a little difficult to know how to help. can you elaborate at little? Guy PS you might find running 'Flagstat tabulate descriptive stats for BAM datset' on your BAM file. Th ...
written 18 days ago by Guy Reeves770
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Comment: C: Making a Pedigree file
... if you are following a tutorial isn't the file avalible? ...
written 18 days ago by Guy Reeves770
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Comment: C: Making a Pedigree file
... There is no tool for this you will need to create it in a text editor outside galaxy and then upload it. It is a simple tabular format described in http://www.shapeit.fr/pages/m02_formats/pedmap.html I think the first 5 columns are obligatory but the rest are not. It kind of depends what you want ...
written 20 days ago by Guy Reeves770
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Comment: C: Proxy Error on importing files by FTP
... would changing this setting in the 'galaxy.ini' file help ? # If large database query results are causing memory or response time issues in # the Galaxy process, leave the result on the server instead. This option is # only available for PostgreSQL and is highly recommended. #database_engine_optio ...
written 25 days ago by Guy Reeves770
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Comment: C: Proxy Error on importing files by FTP
... HI Currently, we are trying 98 files at a time ( about 0.5Gb each). But in the past I have done this with 400 at a time with no problem. I have been told currently that if they drop to doing 8 at a time there is less or no problem. We are using the same instance successful with 400 at a time a ...
written 26 days ago by Guy Reeves770
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Comment: C: What Galaxy tools can preprocess VCF file before running the SNPEff annotation p
... Snpeff should accept any properly formed vcf. There should be no need to preprocess it. Is data type = vcf? What is the problem you are having? ...
written 4 weeks ago by Guy Reeves770

Latest awards to Guy Reeves

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How to successfully export large numbers of files outside of galaxy- as history
Scholar 6 weeks ago, created an answer that has been accepted. For A: increasing the number of concurent jobs that can be run
Scholar 7 months ago, created an answer that has been accepted. For A: increasing the number of concurent jobs that can be run
Voter 17 months ago, voted more than 100 times.
Scholar 17 months ago, created an answer that has been accepted. For A: Without 'Available inputs are:' it is not possible to rename datasets in workflo
Scholar 17 months ago, created an answer that has been accepted. For A: Attaching annotations to Sequences
Centurion 18 months ago, created 100 posts.
Scholar 21 months ago, created an answer that has been accepted. For A: Attaching annotations to Sequences
Student 24 months ago, asked a question with at least 3 up-votes. For What is the ROD file -Need help with "Realigner Target Creator" tool
Rising Star 2.0 years ago, created 50 posts within first three months of joining.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: variable inputs workflow
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Student 2.2 years ago, asked a question with at least 3 up-votes. For What is the ROD file -Need help with "Realigner Target Creator" tool

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