User: aays
aays • 140
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Grad student in evolutionary genomics.
Posts by aays
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... 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 9 weeks ago by
aays • 140
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... Happy to help! And thanks for sharing the plot - looks fantastic :) ...
written 9 weeks ago by
aays • 140
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... 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 9 weeks ago by
aays • 140
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... 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 5 months ago by
aays • 140
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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 5 months ago by
aays • 140
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... [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 5 months ago by
aays • 140
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... 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 7 months ago by
aays • 140
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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 7 months ago by
aays • 140
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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 9 months ago by
aays • 140
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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 14 months ago by
aays • 140
Latest awards to aays
Appreciated
9 weeks ago,
created a post with more than 5 votes.
For A: error with add_theme function ggplot2 (R)
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: error with add_theme function ggplot2 (R)
Teacher
9 weeks ago,
created an answer with at least 3 up-votes.
For A: error with add_theme function ggplot2 (R)
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