User: Guy Reeves

gravatar for Guy Reeves
Guy Reeves1.0k
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Joined:
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Email:
r*****@evolbio.mpg.de

Posts by Guy Reeves

<prev • 240 results • page 1 of 24 • next >
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Answer: A: Spliting a VCF for some genotypes
... Hi This tool should do it 'VCFselectsamples: Select samples from a VCF dataset'. there are others. It may help when looking for tools to be aware of VCF terminology specifically that individuals = samples. 'genotypes' could mean a few different things, Personally I use this galaxy tool 'Select ...
written 11 months ago by Guy Reeves1.0k
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Answer: A: Is it possible to specify the download folder to be on the server hosting the ga
... Update nothing came of the tool request and the tool mentioned above looks perfect but there is no help about how to use it ( I did contact the author a few times about writing a very short description of how to set up the tool) https://toolshed.g2.bx.psu.edu/view/earlhaminst/export_to_cluster/ I ...
written 11 months ago by Guy Reeves1.0k
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Comment: C: How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads
... though I may not have fully understood ...
written 13 months ago by Guy Reeves1.0k
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Answer: A: How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads
... If you have data as described in edit 1 which is limited to V(D)J loci you are correct you cannot do a 'a full transcriptome analysis' as it would have no data about other genes. Cheers Guy ...
written 13 months ago by Guy Reeves1.0k
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Comment: C: How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads
... Hi we often noticed that 2x 300bp reads give lower than anticipated mapping. It is my understanding that all mapping programs essentially have an absolute cut off for mapping rather than a % of their length(because of the way k-mers are used). So the default cut off for mapping might be 2 bp rega ...
written 13 months ago by Guy Reeves1.0k
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Answer: A: Counting number of times multiple defined values appear in the dataset
... If you want to count the number of variants in genes then SNPeff. gives such a report for genes. This will be possible on usegalaxy.org if you are working with a reference genomes which is already present as a drop down option. What you want to do seams easy but I cannot think of another way off ...
written 14 months ago by Guy Reeves1.0k
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Comment: C: Running FreeBayes to a collection of BAM files individually
... If I understand what you want to do the Tag idea will not be helpful. Also the concern about missing data in my original reply probably also does not apply ...
written 14 months ago by Guy Reeves1.0k
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Answer: A: Running FreeBayes to a collection of BAM files individually
... I guess the key part of your message is "my goal was identifying the sample(s) where each sample comes from (the BAM file or so". If I understand correctly. what about modifying the SM: in the BAM file headers so that each BAM has a unique SM:. For an individual X. with 3 BAMs with each having ...
written 14 months ago by Guy Reeves1.0k
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Answer: A: Running FreeBayes to a collection of BAM files individually
... Freebayes is like GATK a joint variant caller, it uses information from multiple samples to asses the likelihood that a real variant exists. That is its strength. If you wish to run it sample by sample you will likely get lots of missing information. If in sample A POSition 100 is 0/0 and in for ...
written 14 months ago by Guy Reeves1.0k
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Comment: C: VCF combine only showing chromosome 1 in the output
... Combining two VCFs I did this https://www.dropbox.com/s/cm0z305ezc3yxyo/Screen%20Shot%202017-07-13%20at%2007.58.01.png?dl=0 and got https://www.dropbox.com/s/idr09tsb5ieezx1/Screen%20Shot%202017-07-13%20at%2007.58.24.png?dl=0 !There us a difference between combine and merge ! ...
written 15 months ago by Guy Reeves1.0k

Latest awards to Guy Reeves

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Cannot set metadata on .bcf output from mpileup
Popular Question 4 months ago, created a question with more than 1,000 views. For Need help with "Reorder SAM/BAM" tool
Popular Question 9 months ago, created a question with more than 1,000 views. For Need help with "Reorder SAM/BAM" tool
Popular Question 10 months ago, created a question with more than 1,000 views. For 'Hidden' Galaxy features which are really useful /AddOrReplaceReadGroups -autoasign
Popular Question 12 months ago, created a question with more than 1,000 views. For Do you know how to filter a .vcf to only return positions with simple SNPs?
Popular Question 13 months ago, created a question with more than 1,000 views. For How to calculate SNP density for sliding windows across a VCF file in galaxy?
Popular Question 14 months ago, created a question with more than 1,000 views. For Need help with "Reorder SAM/BAM" tool
Popular Question 15 months ago, created a question with more than 1,000 views. For Need help with "Reorder SAM/BAM" tool
Guru 15 months ago, received more than 100 upvotes.
Teacher 15 months 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
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Scholar 18 months ago, created an answer that has been accepted. For A: How to successfully export large numbers of files outside of galaxy- as history
Teacher 19 months 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 19 months ago, created an answer that has been accepted. For A: increasing the number of concurent jobs that can be run
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Scholar 2.9 years ago, created an answer that has been accepted. For A: Without 'Available inputs are:' it is not possible to rename datasets in workflo

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