Moderator: JC
JC ♦ 9.1k
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- Location:
- Mexico
- Website:
- http://about.me/jcabal...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 19 hours ago
- Joined:
- 7 years, 6 months ago
- Email:
- j*******************@gmail.com
Computational Biologist
Posts by JC
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... Many normalization methods don't preselect genes, for example, TMM algorithm in EdgeR looks for the more stable genes in your data. ...
written 3 days ago by
JC ♦ 9.1k
1
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88
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... Check how to write to file in python https://www.guru99.com/reading-and-writing-files-in-python.html ...
written 5 days ago by
JC ♦ 9.1k
2
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0
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72
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Comment:
C: Hg38 to b37 LiftOver chain?
... The UCSC doesn't provide liftOver to b37, you can use hg19 instead unless you expect differences in your analysis, here is an explanation of the different version: https://software.broadinstitute.org/gatk/documentation/article?id=23390 ...
written 5 days ago by
JC ♦ 9.1k
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118
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... glad to help, good luck with your research ...
written 5 days ago by
JC ♦ 9.1k
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152
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2
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... yes, it could be a cause of the filtering ...
written 5 days ago by
JC ♦ 9.1k
2
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2
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118
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... I wouuld use a Perl (or Python script) to parse the multifasta and run your tool, like:
#!/usr/bin/perl
use strict;
use warnings;
$/="\n>"; # read fasta sequences in blocks
while (<>) {
s/>//g;
my ($id, @seq) = split (/\n/, $_);
m ...
written 6 days ago by
JC ♦ 9.1k
1
vote
3
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151
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3
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... here how I could do in Perl:
#!/usr/bin/perl
use strict;
use warnings;
$ARGV[2] or die "use convert.pl ref_data fasta_in fasta_out\n";
my $ref_file = shift @ARGV;
my $in_file = shift @ARGV;
my $out_file = shift @ARGV;
my %code = ();
my @aa = (); ...
written 6 days ago by
JC ♦ 9.1k
0
votes
2
answers
152
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2
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... The base call is performed independently, some sequencers remove low-quality reads without removing the respective pair, so you will end with singletons. ...
written 7 days ago by
JC ♦ 9.1k
3
votes
2
answers
92
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2
answers
... $ sort -g -k2 list
A 1.14e-06
B 4.35e-05
C 0.5361
D 0.7278 ...
written 8 days ago by
JC ♦ 9.1k
0
votes
3
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151
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3
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... this looks like a homework ... otherwise please explain why do you need the file in your research or offer to pay at least a coffee for a script ... ...
written 12 days ago by
JC ♦ 9.1k
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