User: Juke-34
Juke-34 • 1.7k
- Reputation:
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- Sweden
- Last seen:
- 5 hours ago
- Joined:
- 4 years, 5 months ago
- Email:
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Posts by Juke-34
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... Good job contacting them was the thing to do.
So it is not the same library as the one described by chipster ( SMARTer Stranded Total RNA ) ...
written 2 days ago by
Juke-34 • 1.7k
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... I have attended a [codeRefinery][1] workshop and I really enjoyed it. I really recommend.
**The theme in short:** The main part focuses on git and is adapted for beginner as well as middle level git users (git expert you can pass your way).
Then they introduce to Reproducible research with Workflow ...
written 3 days ago by
Juke-34 • 1.7k
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... I guess yes firststrand (RF) sounds the one to use then. ...
written 3 days ago by
Juke-34 • 1.7k
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... It is not a 'noob question' and a real problem. It's good that you realise that. Most people do not pay attention to it. They don't realise that different annotations exist and just take the one by default that is the NCBI one.
That being said it's really hard to compare annotation and say which o ...
written 7 days ago by
Juke-34 • 1.7k
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Comment:
C: Merging 2 GFF files
... Adding extra character is enough and probably the easiest. If you have already done downstream analysis with snpEff I don't know what it might imply. If it was using the IDs I guess it would have complain to meet duplicate IDs. ...
written 7 days ago by
Juke-34 • 1.7k
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157
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Comment:
C: Maker Gff3 file issues
... Sounds like a line in your file is not 9 columns. That cannot be fixed by the tool. You have to find this line manualy ( the one cited in the error) and fix it.
I have already seen that... it’s rare but few times one line is split and written over 2 lines ... ...
written 15 days ago by
Juke-34 • 1.7k
1
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Answer:
A: Gff3 file issues
... I got often this kind of problem using MAKER on our cluster (LSF + openMPI). I never succeeded to find where the problem is coming from.
I end up with some parent features missing or duplicated features.
I have developed a library to standardise any kind of GTF/GFF that fix all kind of problem and ...
written 16 days ago by
Juke-34 • 1.7k
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217
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... Probably using bioperl will ease your life:
use Bio::SeqIO;
use strict;
use warnings;
my $fasta = Bio::SeqIO->new(-file => $file , -format => 'Fasta');
while ( my $seq = $fasta->next_seq() ) {
my $header = $seq->id;
if ($header =~ m/ >(.+)/){
...
written 20 days ago by
Juke-34 • 1.7k
1
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217
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... while (my $line = <$IN>) {
if ($header =~ m/ >(.+)/){
print "My species name = $1\n";
}
} ...
written 20 days ago by
Juke-34 • 1.7k
1
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... it depends, they don’t care if it’s repeat element or not, they just care about the length of sequences. What I remember it’s that they ask to motivate your choice when you want to keep short sequences/contigs <100 bp. The best approach would be to keep all of them then when you have your embl fl ...
written 4 weeks ago by
Juke-34 • 1.7k
Latest awards to Juke-34
Scholar
16 days ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Popular Question
12 weeks ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar
5 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Good Answer
9 months ago,
created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
Appreciated
10 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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12 months ago,
voted at least 25 times.
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Scholar
13 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Teacher
13 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Commentator
15 months ago,
created a comment with at least 3 up-votes.
For C: How to manipulate a gff or gtf file manually?
Guru
15 months ago,
received more than 100 upvotes.
Appreciated
21 months ago,
created a post with more than 5 votes.
For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Teacher
21 months ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher
2.1 years ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Teacher
2.2 years ago,
created an answer with at least 3 up-votes.
For A: Where is it possible to submit annotated eukaryote genomes?
Centurion
2.5 years ago,
created 100 posts.
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