Differences

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--- functional_annotation_with_the_funannotate_pipeline [2025/01/28 10:31] – 134.190.225.16
+++ functional_annotation_with_the_funannotate_pipeline [2025/12/09 13:02] (current) – [EggNOG mapping] 134.190.190.181
@@ Line 15: / Line 15: @@
 **Important note!!!**
-Before proceeding you need to check your gff3 file for errors by running ''validate_gene_models_in_gff3.py''
+Before proceeding you need to check your gff3 file for errors by running ''validate_gene_models_in_gff3.py''. (Activate the gffutils environment to run this script, you may also have to comment out the ''import regex as re'' line if you're not checking Blastocystis genomes.
-This script will locate errors in your gff3 file that often occur due to manual editing (premature stop codons, incorrect exon numbering, missing start and stop codons, start or stop location not matching exon location, etc).  Incorrect phase designation for an exon can lead to premature stop codons so keep that in mind when looking for cause of premature stops.
+This script will locate errors in your gff3 file that often occur due to manual editing (premature stop codons, incorrect exon numbering, missing start and stop codons, start or stop location not matching exon location, etc).  Incorrect phase designation for an exon can lead to premature stop codons so keep that in mind when looking for causes of premature stops.
@@ Line 97: / Line 97: @@
 #$ -cwd
 #$ -q 256G-batch
-#$ -m bea
-#$ -M joran.martijn@dal.ca
 #$ -pe threaded 40