User: Guy Reeves

gravatar for Guy Reeves
Guy Reeves1.0k
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Posts by Guy Reeves

<prev • 236 results • page 1 of 24 • next >
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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 12 hours 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 6 weeks 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 7 weeks 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 7 weeks 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 7 weeks 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 9 weeks ago by Guy Reeves1.0k
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Answer: A: VCF combine only showing chromosome 1 in the output
... If you post the shared link to the history here that may also help me help you. ...
written 9 weeks ago by Guy Reeves1.0k
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Comment: C: VCF combine only showing chromosome 1 in the output
... I just tried this tool and I get only one output file and one log file. ...
written 9 weeks ago by Guy Reeves1.0k
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Comment: C: VCF combine only showing chromosome 1 in the output
... what is the difference between combine versus merge VCF? ...
written 9 weeks ago by Guy Reeves1.0k
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Answer: A: VCF combine only showing chromosome 1 in the output
... Hi Siri Can I sugest you try another tool. I am assuming that you are using usegalaxy.org. So I suggest you try "Combine Variants (Galaxy Version 0.0.4)" and see if you get the same result. If you are using your own galaxy instance there are a number of other tools you could try Tell us what ha ...
written 10 weeks ago by Guy Reeves1.0k

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Popular Question 15 days 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 7 weeks ago, created a question with more than 1,000 views. For Need help with "Reorder SAM/BAM" tool
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