From 97b8913ef0d6306a655560cb745b2b18ce070b17 Mon Sep 17 00:00:00 2001 From: Anna Syme Date: Wed, 16 Oct 2024 11:17:25 +1100 Subject: [PATCH] Update Helixer tutorial.md - gffread inputs In the tutorial, for the tool gffread, for `select fasta outputs`, I think the wrong item is specified. I have changed it from `fasta file with spliced exons` to `protein fasta file`, because the next step in the tutorial (using Busco) needs this protein fasta file. --- topics/genome-annotation/tutorials/helixer/tutorial.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/topics/genome-annotation/tutorials/helixer/tutorial.md b/topics/genome-annotation/tutorials/helixer/tutorial.md index 468730c7d242ef..011250ee4adee2 100644 --- a/topics/genome-annotation/tutorials/helixer/tutorial.md +++ b/topics/genome-annotation/tutorials/helixer/tutorial.md @@ -170,7 +170,7 @@ We want to run BUSCO on the protein sequences predicted from gene sequences of t > - {% icon param-file %} *"Input GFF3 or GTF feature file"*: output of {% tool [Helixer](toolshed.g2.bx.psu.edu/repos/genouest/helixer/helixer/0.3.3+galaxy1)) %} > - In *"Reference Genome"* select: `From your history` (Input dataset) > - *"Genome Reference Fasta"*: `masked genome` (Input dataset) -> - In *"Select fasta outputs"* select: `fasta file with spliced exons for each GFF transcript (-y)` +> - In *"Select fasta outputs"* select: `protein fasta file with the translation of CDS for each record (-y)` > - *"full GFF attribute preservation (all attributes are shown)"*: `Yes` > - *"decode url encoded characters within attributes"*: `Yes` > - *"warn about duplicate transcript IDs and other potential problems with the given GFF/GTF records"*: `Yes`