User: aays

gravatar for aays
aays140
Reputation:
140
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Location:
Canada
Last seen:
4 months, 3 weeks ago
Joined:
1 year, 11 months ago
Email:
a**********@mail.utoronto.ca

Grad student in evolutionary genomics.

Posts by aays

<prev • 19 results • page 1 of 2 • next >
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Comment: C: samtools mpileup `error uninitialized value $l in numeric lt` during BAM to FAST
... I'm not too sure what happened here, but seems other people have had similar problems. [This thread][1] might be worth going through - lists a couple potential issues that may be causing this. Someone also found a solution [here][2]. [1]: http://seqanswers.com/forums/showthread.php?t=47471 [2] ...
written 11 months ago by aays140
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Comment: C: error with add_theme function ggplot2 (R)
... Happy to help! And thanks for sharing the plot - looks fantastic :) ...
written 11 months ago by aays140
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Answer: A: error with add_theme function ggplot2 (R)
... I think the issue wrt your error is happening here: > sp2<-sp+theme(legend.key.size = unit(0.15, "cm")) + + theme(legend.text = element_text(size = 4)) + facet_wrap(~sample) > +theme(legend.key.size=unit(0.9, "cm")) + theme(legend.text = + element_text(size = 10)) + theme ...
written 11 months ago by aays140
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Comment: C: Implement p-values and significance levels in boxplots for more of two groups wi
... If I understand the question correctly, you may want to explore [the `ggsignif` package](https://github.com/const-ae/ggsignif), which I believe extends `ggplot2`'s functionality for the addition to significance bars as single geoms. ...
written 14 months ago by aays140
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Answer: A: bcftools to GATK
... On the surface, this very much seems like a bug - I'm not too familiar with the inner workings of GATK, but the final bit of that error message is telling me that some kind of object coercion is going on when it shouldn't be. However, this may also have to do with the fact that (iirc) CombineGVCFs c ...
written 14 months ago by aays140
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Answer: A: How to extract PRDM9 binding motifs in bed format?
... [EMBOSS fuzznuc](http://emboss.sourceforge.net/apps/cvs/emboss/apps/fuzznuc.html) might solve your issue. The output isn't exactly in bed format, but it does return start/end coordinates in a table-formatted file and also allows for fuzzy searching, which is probably handy considering the degeneracy ...
written 14 months ago by aays140
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Comment: C: How to get the coordinations of CpG sites in non-human genome
... What format is your data in? FASTA, I presume? If so, this is something that can be handled with a short homemade Python script, iterating through the sequence and writing instances of CG dinucleotide pairs into an output file. I'd be happy to throw something along those lines together if that's t ...
written 16 months ago by aays140
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Comment: C: CpG Island prediction
... I don't know if you're still looking for an answer to this, but I've found some success with [CpGcluster 1.0](https://github.com/RatneshSingh/crude-perl-scripts/blob/master/CpGcluster.pl). It also doesn't have any of the constraints you've mentioned here iirc. ...
written 16 months ago by aays140
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Comment: C: Trouble indexing a .vcf.gz file
... If the file is sorted by position, that's a strange error to get, and I wouldn't think that the chromosome field has much to do with it necessarily. Like the error says, does explicitly adding the -p option help? Like so: tabix -p vcf myFile.vcf.gz Beyond that, was it compressed using bgzip? ...
written 18 months ago by aays140
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Answer: A: How to get fasta by gene id
... Have you tried using Biopython? The task more or less boils down to this with that: import time from Bio import Entrez Entrez.email = [your email] def fetch(id): handle = Entrez.efetch(db = 'protein', id = id, retmode = 'fasta', rettype = 'text') seq = handle.read() ...
written 23 months ago by aays140

Latest awards to aays

Appreciated 11 months ago, created a post with more than 5 votes. For A: error with add_theme function ggplot2 (R)
Scholar 11 months ago, created an answer that has been accepted. For A: error with add_theme function ggplot2 (R)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: error with add_theme function ggplot2 (R)

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