Moderator: JC
JC ♦ 6.8k
- Reputation:
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- Location:
- Mexico
- Website:
- http://about.me/jcabal...
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- Google Scholar Page
- Last seen:
- 2 days, 3 hours ago
- Joined:
- 6 years, 3 months ago
- Email:
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Computational Biologist
Posts by JC
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... There are several ways to do this, also there are unknown conditions, do you need all words including overlapped words? Do you care for words in the reverse-complement chain? The simplest solution I can think is to split your sequences and count array elements:
#!/usr/bin/perl
use stri ...
written 26 days ago by
JC ♦ 6.8k
3
votes
2
answers
152
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2
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Answer:
A: Rstudio like IDE for perl
... I use Perl for many things, but I still just use regular text editors (right now I'm using [Atom][1]). The only Perl IDE I remember is [ActivePerl][2].
Or you can use [Jupyter][3] and add Perl [kernels][4]
[1]: https://atom.io/
[2]: https://www.activestate.com/activeperl
[3]: http://jupyte ...
written 4 weeks ago by
JC ♦ 6.8k
3
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0
answers
161
views
0
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... Those are field sports ;)
But what are you plotting is the contribution per dimension (that's why is an arrow or vector), for example, the values in Shot.put are correlated with an increase in Dimension 1, or 110m.hurdle is inversely correlated to the same axis. Remember that a PCA is a projection, ...
written 5 weeks ago by
JC ♦ 6.8k
1
vote
1
answer
113
views
1
answers
... You can use VCFtools https://vcftools.github.io/index.html, it also contains Perl modules ...
written 7 weeks ago by
JC ♦ 6.8k
4
votes
0
answers
133
views
0
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Comment:
C: Fastq file download from pubmed
... Nothing is wrong with your file, it's a Fastq file which encodes the nucleotidic sequence and their quality, the "%" is a low-quality value in Phred+33 scale. Check https://en.wikipedia.org/wiki/FASTQ_format ...
written 8 weeks ago by
JC ♦ 6.8k
1
vote
2
answers
293
views
2
answers
Comment:
C: How to use igv on ubuntu
... open a terminal and type `igv` ...
written 9 weeks ago by
JC ♦ 6.8k
2
votes
2
answers
293
views
2
answers
Answer:
A: How to use igv on ubuntu
... If you are using Ubuntu 18.04 you can do `sudo apt install igv`
For previous versions you need something like:
sudo apt install default-jre
curl -LO http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.10.zip
unzip IGV_2.4.10.zip
cd IGV_2.4.10
sudo ln -s $PWD/igv.s ...
written 9 weeks ago by
JC ♦ 6.8k
4
votes
5
answers
264
views
5
answers
... just for fun:
#!/usr/bin/perl
use strict;
use warnings;
$/ = "\n>";
while (<>) {
s/>//g;
my ($id, @seq) = split (/\n+/, $_);
my @slices = split (/N+/, join("", @seq));
my $num = 0;
foreach my $seq (@slices) {
...
written 9 weeks ago by
JC ♦ 6.8k
2
votes
1
answer
137
views
1
answers
... In general, such positions are ignored. ...
written 9 weeks ago by
JC ♦ 6.8k
0
votes
3
answers
177
views
3
answers
... Glad to help, how large was the data? ...
written 10 weeks ago by
JC ♦ 6.8k
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