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I would also be very interested in generating a gtf file for arabidopsis. Would it be possible to post the code ?
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Download TAIR10_GFF3_genes.gff inTAIR, and then use the Perl script below to convert this gff file to gtf which is used as conference annotation Cufflinks.
#!/usr/bin/perl
use warnings;
use strict;
while (<>) {
chomp;
my @parts = split /\t/;
if ( !(($parts[2] eq 'three_prime_UTR')|($parts[2] eq 'five_prime_UTR')|($parts[2] eq 'exon')|($parts[2] eq 'CDS')) ) {
next;
}
elsif ( $parts[2] eq 'three_prime_UTR') {
$parts[2] = '3UTR';
}
elsif ($parts[2] eq 'five_prime_UTR') {
$parts[2] = '5UTR';
}
$parts[8] =~ s/^Parent=((\w+)\.\w*).*/gene_id \"$2\"; transcript_id \"$1\";/sg;
$_ = join "\t" , @parts;
print "$_\n";
}Comment
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celeste8, thank you very much !Comment
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Thanks, celeste8!!
Sam Hokin
Computational Scientist, Carnegie and NCGRComment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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