User: jason

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jason160
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Posts by jason

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Comment: C: Parse GFF to infer numbers of all exons, and just coding exons per gene
... yes I leave it as an exercise to the reader to add/replace the 'CDS' part with 'exon' above or modify the code to track both CDS and exon ... ...
written 4.3 years ago by jason160 • updated 3 months ago by RamRS25k
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Answer: A: Parse GFF to infer numbers of all exons, and just coding exons per gene
... Assuming well behaved GFF3 this perl code gets you there. $ perl count_CDS.pl annotation.gff3 my %genes; while(<>) { chomp; my @row = split(/\t/,$_); next unless $row[2] eq 'CDS'; my %group = map { split(/=/,$_) } split(/;/,pop @row); $genes{$group{Parent}}++; } #sorted by genes with ...
written 4.3 years ago by jason160
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Answer: A: What is the difference between GTF AND GFF format
... I think it is explained [here][1] pretty well. GTF is a specific instance of the [GFF version 2 format][2]. A flavor of GTF that [they are calling 2.2][3] includes specific 9th column terms `transcript_id`, `protein_id`, `gene_id` My experience has been GTF 2.2 version works well with TopHat. ...
written 5.8 years ago by jason160 • updated 17 months ago by RamRS25k
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Answer: A: Removing branch support values that meet certain requirements in a newick file
... use Bio::TreeIO; use strict; my $in = Bio::TreeIO->new(-format => 'newick', -fh => \*DATA); # replace above with this to open a file # my $in = Bio::TreeIO->new(-format => 'newick', -file => "mytree.tre"); # see Bio::TreeIO on how you can write directly to a file, otherwise t ...
written 5.8 years ago by jason160

Latest awards to jason

Scholar 4.3 years ago, created an answer that has been accepted. For A: Removing branch support values that meet certain requirements in a newick file
Good Answer 5.6 years ago, created an answer that was upvoted at least 5 times. For A: What is the difference between GTF AND GFF format
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: What is the difference between GTF AND GFF format
Appreciated 5.8 years ago, created a post with more than 5 votes. For A: What is the difference between GTF AND GFF format
Scholar 5.8 years ago, created an answer that has been accepted. For A: Removing branch support values that meet certain requirements in a newick file
Teacher 5.8 years ago, created an answer with at least 3 up-votes. For A: What is the difference between GTF AND GFF format

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