Moderator: JC
JC ♦ 6.6k
- Reputation:
- 6,640
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- Location:
- Mexico
- Website:
- http://about.me/jcabal...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 5 days, 12 hours ago
- Joined:
- 6 years, 1 month ago
- Email:
- j*******************@gmail.com
Computational Biologist
Posts by JC
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Comment:
C: How to use igv on ubuntu
... open a terminal and type `igv` ...
written 5 days ago by
JC ♦ 6.6k
2
votes
2
answers
124
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 6 days ago by
JC ♦ 6.6k
3
votes
5
answers
168
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 6 days ago by
JC ♦ 6.6k
2
votes
1
answer
86
views
1
answers
... In general, such positions are ignored. ...
written 6 days ago by
JC ♦ 6.6k
0
votes
3
answers
140
views
3
answers
... Glad to help, how large was the data? ...
written 13 days ago by
JC ♦ 6.6k
0
votes
3
answers
140
views
3
answers
... You can use perl or python to get that:
#!/usr/bin/perl
use strict;
use warnings;
my %g = ();
my $a = undef;
my $b = undef;
my $net = 0;
my $fst = 1;
while (<>) {
chomp;
($a, $b) = split (/\s+/, $_);
if ($fst == 1) {
...
written 16 days ago by
JC ♦ 6.6k
0
votes
2
answers
142
views
2
answers
... Cancer is highly variable, even tumours from the same patient are different, you can see this in a PCA or similar plot. So it's not surprising that you get 6k DEG, beside FC, you can also filter by the number of samples sharing the gene as DEG, like filtering by genes as DE in 50% of your samples. ...
written 16 days ago by
JC ♦ 6.6k
1
vote
1
answer
119
views
1
answers
Answer:
A: Bioconductor - DESeq
... Answering your 3 questions:
1. Yes, you can compare Acinar (A), Duct (D) and controls (C) but I would contrast (A / C) vs (D / C) and then get DEG between groups, that will mean to get genes differentially expressed to the control and differential expressed between A / D. But if you only care about ...
written 18 days ago by
JC ♦ 6.6k
0
votes
1
answer
119
views
1
answers
Comment:
C: Bioconductor - DESeq
... Hi Soheila, I just formatted your post and tagged as Question, because this is not a "Tutorial". ...
written 18 days ago by
JC ♦ 6.6k
0
votes
1
answer
136
views
1
answers
... I'm assuming that you want to convert each VCF record into the genetic variant observed, so "0/0" is considered "C" and "1/1" is "A" and "0/1" is "CA".
#!/usr/bin/perl
use strict;
use warnings;
while (<>) {
if (/^#/) {
print;
next;
}
...
written 4 weeks ago by
JC ♦ 6.6k
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