Moderator: JC
JC ♦ 7.6k
- Reputation:
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- Location:
- Mexico
- Website:
- http://about.me/jcabal...
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 days, 3 hours ago
- Joined:
- 6 years, 10 months ago
- Email:
- j*******************@gmail.com
Computational Biologist
Posts by JC
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... if the gene models are correct and you want only to quantify known genes, it is perfectly fine. ...
written 3 days ago by
JC ♦ 7.6k
1
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... if there are no big bias yes, after processing just check libraries in a PCA, if there are no big differences you can merge them ...
written 3 days ago by
JC ♦ 7.6k
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138
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... A simple book could be hard to create, each methodology is based on a lot of biological knowledge. Even biologists don't understand the methods they do, many experiments are based on "faith". Coming from a wet lab I know many people cannot explain the methods, like "don't do a PCR on a moon night be ...
written 4 days ago by
JC ♦ 7.6k
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Comment:
C: transcripts assemble by StringTie
... are you using:
ftp://ftp.ensemblgenomes.org/pub/release-42/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC.dna.toplevel.fa.gz
ftp://ftp.ensemblgenomes.org/pub/release-42/plants/gtf/triticum_aestivum/Triticum_aestivum.IWGSC.42.gtf.gz
? ...
written 6 days ago by
JC ♦ 7.6k
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6
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... true, I modify the code to read the file name from another var ...
written 10 days ago by
JC ♦ 7.6k
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6
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242
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6
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... The `while (<$infile>) {}` loop reads the file line per line ...
written 10 days ago by
JC ♦ 7.6k
0
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1
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82
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Answer:
A: fastq reads cleaning
... Any good bioinformatician will run a QC before doing anything and perform cleaning if needed. I think it is omitted because of that and recent Illumina protocols returns cleaned reads. I don't remember last time I cleaned some Illumina data since the HiSeq 2000. ...
written 11 days ago by
JC ♦ 7.6k
0
votes
2
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141
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2
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Comment:
C: transcripts assemble by StringTie
... Sadly, even when the genome and version are named equally in NCBI and Ensembl, the sequences names could be different. Use genome and annotation from the same source to ensure you have the same naming. ...
written 11 days ago by
JC ♦ 7.6k
1
vote
6
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242
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6
answers
... There are some Perl-ings you need to understand first:
my $infile = $ARGV[0];
This line reads the first command line argument after your script name and pass to the variable **$infile**
open (my $infile, "<", "namconvmars.txt")
or die "Can't read from $infile: $!";
You are declar ...
written 11 days ago by
JC ♦ 7.6k
1
vote
2
answers
85
views
2
answers
... Perl:
#!/usr/bin/perl
use strict;
use warnings;
my $head = '';
while (<>) {
chomp;
if (/^(@.+)/) { $head = $1; }
else { print "$_\t$head\n"; }
}
Run as `perl addheader.pl < INPUT > OUPUT` ...
written 11 days ago by
JC ♦ 7.6k
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