Load the landmarks¶
First, load the landmark scaffolds. The repo includes a FASTA file with scaffold names only, no sequences, for this purpose. Use the FASTA loader as described in the mRNA section: you do not need to define a parent relationship. You can use the SO term contig for the type.
Load the GFF file¶
Consider the example GFF file below.
##gff-version 3 Contig0 FRAEX38873_v2 gene 16315 44054 . + . ID=FRAEX38873_v2_000000010;Name=FRAEX38873_v2_000000010;biotype=protein_coding Contig0 FRAEX38873_v2 mRNA 16315 44054 . + . ID=FRAEX38873_v2_000000010.1;Parent=FRAEX38873_v2_000000010;Name=FRAEX38873_v2_000000010.1;biotype=protein_coding;AED=0.05 Contig0 FRAEX38873_v2 five_prime_UTR 16315 16557 . + . ID=FRAEX38873_v2_000000010.1.5utr1;Parent=FRAEX38873_v2_000000010.1 Contig0 FRAEX38873_v2 exon 16315 16967 . + . ID=FRAEX38873_v2_000000010.1.exon1;Parent=FRAEX38873_v2_000000010.1 Contig0 FRAEX38873_v2 CDS 16558 16967 . + 0 ID=FRAEX38873_v2_000000010.1.cds1;Parent=FRAEX38873_v2_
The below table explains each column.
|1||seqid||Name of the landmark chromosome or scaffold (not the feature itself).||Contig0|
|2||source||Program name, data source, etc||FRAEX38873_v2|
|3||type||Sequence ontology term for type_id of feature||gene|
|4||start||start of the feature.||16315|
|5||end||end of the feature.||44054|
|6||score||Float value or . The score, because the feature was computationally predicted. ignore.||.|
|7||strand||Can be = or -. Refers to the strand of DNA: ignore||+|
|8||phase||Can be 0, 1, 2, or . Refers to the open reading frame, you can ignore.||.|
|9||attributes||This includes the actual name for the feature that will be created (in this case FRAEX38873_v2_000000010). It also includes the Parent= tag.||ID=FRAEX38873_v2_000000010;Name=FRAEX38873_v2_000000010;biotype=protein_coding|
Every line of the GFF file will result in a new feature. The above example will create gene, mRNA, five_prime_UTR, exon, CDS, and protein features (see below for how to skip protein creation). If you’d like to not load five_prime_UTR features, for example, delete them from the file beforehand.
The GFF Importer¶
First, upload the file. In order to use the GUI uploader, the file extension should be
.gff3. See below for information on GFF types.
The landmark is the Chado feature on which the individual features are being mapped. This is typically a scaffold, contig, or chromosome (we chose contig above). If your landmarks are not uniquely named for this organism, you can specify the type here.
As before, you may need to specify a regexp so that your proteins are correctly linked to your mRNA. Note that if you dont specify a protein regexp, it will look for proteins that are [mrna_name]-protein. This could result in new proteins being inserted accidentally! I’ve submitted a change that will allow you to skip creating proteins in this manner, look for it soon.
A note on GFF versions¶
GFF files are not the most uniform files around. There are GFF, GFF2, GTF, and GFF3. The Tripal GFF loader does its best, but it was designed to work withGFF3.