User: Russ

gravatar for Russ
Russ300
Reputation:
300
Status:
Trusted
Location:
Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
Last seen:
4 hours ago
Joined:
3 years ago
Email:
r*******@uoguelph.ca

Posts by Russ

<prev • 39 results • page 1 of 4 • next >
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Answer: C: mRNA Biology Question
... A quick google brought this unreferenced tech note from Qiagen: https://www.qiagen.com/us/resources/faq?id=06a192c2-e72d-42e8-9b40-3171e1eb4cb8&lang=en ...
written 10 days ago by Russ300
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Comment: C: GT (genotype information) in haploid organism has a value of 2 .
... What version of GATK are you using? Did you specify the ploidy of your organism while running the analysis? ...
written 11 days ago by Russ300
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Comment: C: This is a file used in the Circos software. Can someone help me understand what
... Link to the documentation on karyotypes: http://circos.ca/documentation/tutorials/ideograms/karyotypes/ ...
written 11 days ago by Russ300
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Answer: A: index of the residue matched using pairwise2 in biopython
... I took a look at the pairwise2 module but also couldn't find any easy way to obtain the indices of the matches ("|"). I was able to modify the format_alignment method slightly to print a list of indices (that starts at 0) of the pipe operator for this specific example - but I'm not sure how it will ...
written 18 days ago by Russ300
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Answer: A: Difference between FC and LogFC
... I find pictures helpful when thinking about these concepts, so quickly made some visualizations for you. They expand on WouterDeCoster's and h.mon's comments. The figures were made in R using with the following code: #Generate fake data fake <- data.frame("gene" = as.numeric(c(1:50)) ...
written 7 weeks ago by Russ300
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Comment: C: Hisat2 index building taking days even with 40 GB RAM
... You'll have to talk to the sys admin of your cluster if you don't have the privileges to install hisat2. ...
written 8 weeks ago by Russ300
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Comment: C: Hisat2 index building taking days even with 40 GB RAM
... I don't have the computational explanation you're looking for, unfortunately, but I don't think the time to completion scales down linearly in the way you're expecting. I tried building an index with 32GB of RAM and it failed - I think the index build needed to load more data than that into the memo ...
written 8 weeks ago by Russ300
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Comment: C: SNPs to rs format
... In the link I provided above to Ensembl. You will see there is a big table near the bottom of the page. You can filter the results for "sheep" by using the box at the top right of the table. The VCF file is one of the options available there. ...
written 10 weeks ago by Russ300
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Comment: C: SNPs to rs format
... Nice tip, thanks Ram. ...
written 10 weeks ago by Russ300
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Answer: A: SNPs to rs format
... Hi hosein_salehi6 It can be tricky dealing with non-reference species. I quickly wrote a script in python that uses the chromosome and position in the text you posted and queries a VCF file with ovine SNPs (sourced from dbSNP 150 apparently). I assumed your results are tab delimited. I accessed the ...
written 10 weeks ago by Russ300

Latest awards to Russ

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Difference between FC and LogFC
Scholar 7 weeks ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Scholar 11 weeks ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Popular Question 4 months ago, created a question with more than 1,000 views. For Allelic association tests for polyploid data
Teacher 5 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Scholar 8 months ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 8 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Supporter 8 months ago, voted at least 25 times.
Scholar 9 months ago, created an answer that has been accepted. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: StringTie "missing header error" [for both HISAT2 and STAR alignment files]

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