Data loading tips

How can I only load a specific type of feature from my GFF file?

You can use the --type argument for flatfile-to-json.pl

E.g.

flatfile-to-json.pl --type mRNA —gff mygff.gff

This will only load mRNAs from the GFF. Additionally, if you want to filter on the source column of the GFF, you can augment the --type argument with an extra formatted parameter for source --type mRNA:augustus

The --type argument can also be a commas separated list of filters like this.

What if I dont want to load the sequence data for the genome, but I want to display the features?

prepare-refseqs.pl accepts a --sizes parameter, which takes a "chrom.sizes" file which is just a tab separated file with two columns, refseq names and their lengths

This let's you view the genome and the features on the genome without loading the sequence data.

How do I convert GTF to GFF

Since flatfile-to-json.pl does not accept GTF, you can convert your GTF to GFF3. Tools like gffread or gtf2gff3.pl are available

The gffread tool is packaged with cufflinks so simply install cufflinks, then you can run

gffread -E merged.gtf -o- > merged.gff3