Moderator: JC
JC ♦ 7.0k
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- Mexico
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- http://about.me/jcabal...
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- Google Scholar Page
- Last seen:
- 1 day, 20 hours ago
- Joined:
- 6 years, 7 months ago
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Computational Biologist
Posts by JC
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C: Are my methods correct?
... This looks like a homework or a bioinformatics test. Anyway, you can use EdgeR from Bioconductor for all. http://bioconductor.org/packages/release/bioc/html/edgeR.html ...
written 1 day ago by
JC ♦ 7.0k
1
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2
answers
139
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2
answers
... It can be done with Perl:
#!/usr/bin/perl
use strict;
use warnings;
my %seqs;
$/ = "\n>"; # read fasta by sequence, not by lines
while (<>) {
s/>//g;
my ($seq_id, @seq) = split (/\n/, $_);
my $seq = uc(join "", @seq); # rebu ...
written 2 days ago by
JC ♦ 7.0k
2
votes
1
answer
130
views
1
answers
... Your major problem will be uncertainness of reads mapped to more than one location in the genome/transcriptome, definitively you need to align to the genome or transcriptome to remove non-unique reads or apply some strategy to decide origin. Kallisto, Sleuth or Salmon are fast enough to create your ...
written 5 days ago by
JC ♦ 7.0k
1
vote
1
answer
71
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1
answers
... Checking the coordinates for your first pair seems like the human hit is more reliable because it is at the end of a gene, meanwhile the mouse coordinates are in an intergenic region. So, you can filter if the hit clearly comes from a possible expressed region. ...
written 12 days ago by
JC ♦ 7.0k
2
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3
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199
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3
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... That can be done using a Perl-one-liner:
$ perl -lne '(m/>.+\[protein_id=(.+?)\]/) ? print ">$1" : print $_' < seqs.fa
>XP_020098752.1
ATGGTTGCCACTAAGTTGATGATGACCTCTTTAATCTTAGTTCAACTGTGGGTGCTTATGCCACTGATGGCGTGTGGTAC
AACGTTAGATCCCATGAGAGAGAGGTATGAACAATGGATTAGCCGATATAGCCGA ...
written 13 days ago by
JC ♦ 7.0k
0
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3
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199
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3
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... An example of your input file and how do you want the output could be helpful.
BTW I proficient in Perl and Python, still using primarily Perl ;) ...
written 16 days ago by
JC ♦ 7.0k
0
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2
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212
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2
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... The **\w** in Perl matches any alphanumeric char and the underscore, and using **(\w+)** should match any word and stop to the first no-word char (space or new line). If you want to save this in a hash:
#!/usr/bin/perl
use strict;
use warnings;
my %species = ();
while ...
written 16 days ago by
JC ♦ 7.0k
0
votes
4
answers
267
views
4
answers
... Hi, you can get access and more information here https://www.databiology.com/index.php/signup ...
written 17 days ago by
JC ♦ 7.0k
1
vote
4
answers
267
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4
answers
... We cover all of that in our platform https://www.databiology.com/ let me know if you want to know more or a demo ...
written 18 days ago by
JC ♦ 7.0k
0
votes
1
answer
25
views
1
answers
Comment:
C: Perl-Genome Assembly with K-mer
... This looks like your homework or a school project, if that's true, at least try to code something or this will be closed/deleted. ...
written 4 weeks ago by
JC ♦ 7.0k
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For C: What Should I Use Blat For?
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