Moderator: JC
JC ♦ 6.5k
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- Mexico
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- http://about.me/jcabal...
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- Last seen:
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- Joined:
- 5 years, 11 months ago
- Email:
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Computational Biologist
Posts by JC
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... Some assemblers allow you to combine techs as pointed before (Mira assembler for example), but answering your question, yes, it's valid to combine the contigs or scaffolds, just be aware that error rate is different between technologies and some variations could occur when you compare your sequences ...
written 11 days ago by
JC ♦ 6.5k
0
votes
3
answers
125
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3
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... that bash line should work, just define "file_new" or change the name:
for file in *fasta; do perl rand.pl < $file > ${file%.fasta}_subset.fasta; done ...
written 12 days ago by
JC ♦ 6.5k
3
votes
3
answers
125
views
3
answers
... Perl:
#!/usr/bin/perl
use strict;
use warnings;
my %seqs =();
$/="\n>";
while (<>) {
s/>//g;
my ($name, @seq) = split (/\n/, $_);
my ($sp, $id) = split (/\./, $name);
push @{ $seqs{$sp} }, join "\n", ">$name", @se ...
written 12 days ago by
JC ♦ 6.5k
0
votes
0
answers
185
views
0
answers
Comment:
C: Fastq header modification
... Or perl:
perl -pe 's/\*\*barcode\d+\/\d+\/\*\*//' < file_in > file_out ...
written 5 weeks ago by
JC ♦ 6.5k
1
vote
2
answers
184
views
2
answers
... Definitely to be sure you need to check for coverage across all regions, if coverage is good enough and variant calling will have no problems, you can assign the position is reference homogenic. ...
written 6 weeks ago by
JC ♦ 6.5k
1
vote
0
answers
107
views
0
answers
... Hi, let me comment your code and see what exactly do you want to do:
#!/usr/bin/perl -w # "-w" and "use warnings" are equivalents, it's prefered to use the second
use warnings;
use strict;
use 5.010; # You don't need back-compatibility, you can remove this
...
written 6 weeks ago by
JC ♦ 6.5k
0
votes
1
answer
161
views
1
answers
... Cpapaya_113_ASGPBv0.4.annotation_info.txt file contains the annotation and mapping to Arabidopsis ...
written 6 weeks ago by
JC ♦ 6.5k
0
votes
1
answer
161
views
1
answers
... If you are using a reference genome, there probably a gene annotation file (GTF, GFF3). Search in [Phytozome][1] for the annotations and try to see gene coverage, for that you can use Bamtools or similar tools.
[1]: https://phytozome.jgi.doe.gov ...
written 6 weeks ago by
JC ♦ 6.5k
0
votes
4
answers
221
views
4
answers
... hi, not sure what do you want to print, just a "\n" if the line contains a homozygous base? or just for A,A, T,T?
what you need is to extend the last if, something like:
`perl -lne '%a = (); @b = split /,/, $_; foreach $b (@b) { $a{$b}++; }; @b = keys %a; if ($#b > 0) { print } else { print "\n ...
written 11 weeks ago by
JC ♦ 6.5k
1
vote
4
answers
221
views
4
answers
... Another Perl solution:
`perl -lne '%a = (); @b = split /,/, $_; foreach $b (@b) { $a{$b}++; }; @b = keys %a; print if ($#b > 0)' < in.txt`
A,T,A,
G,T,
A,T,A,
T,C,
G,G,G,A,
A,T,G,C ...
written 11 weeks ago by
JC ♦ 6.5k
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