Skip to content
Snippets Groups Projects
Commit a26e1da2 authored by Niko (Nikolaos) Papadopoulos's avatar Niko (Nikolaos) Papadopoulos
Browse files

update files to be used

parent b96bfe8e
Branches
Tags
No related merge requests found
Hide whitespace changes
Inline Side-by-side
08-submission/gff-04-convert_to_embl.sh
+ 2
− 3
View file @ a26e1da2
...@@ -4,13 +4,12 @@ module load conda ...@@ -4,13 +4,12 @@ module load conda
conda activate emblmygff3 conda activate emblmygff3
GENOME=/lisc/project/zoology/pycnogonum/paper/zenodo/results/draft.fasta GENOME=/lisc/project/zoology/pycnogonum/paper/zenodo/results/draft.fasta
GFF=/lisc/scratch/zoology/pycnogonum/genome/submission/merged_sorted_named_dedup_filtered.gff3 GFF=/lisc/scratch/zoology/pycnogonum/genome/submission/merged_sorted_named_dedup_flagged.gff3
RESDIR=/lisc/scratch/zoology/pycnogonum/genome/submission RESDIR=/lisc/scratch/zoology/pycnogonum/genome/submission
cd $RESDIR || exit cd $RESDIR || exit
EMBLmyGFF3 $GFF $GENOME \ EMBLmyGFF3 $GFF $GENOME \
--expose_translations \
--topology linear \ --topology linear \
--molecule_type 'genomic DNA' \ --molecule_type 'genomic DNA' \
--transl_table 1 \ --transl_table 1 \
...@@ -18,7 +17,7 @@ EMBLmyGFF3 $GFF $GENOME \ ...@@ -18,7 +17,7 @@ EMBLmyGFF3 $GFF $GENOME \
--taxonomy INV \ --taxonomy INV \
--locus_tag VPG \ --locus_tag VPG \
--project_id PRJEB80537 \ --project_id PRJEB80537 \
-vvv \ -v \
-o result.embl -o result.embl
gzip result.embl gzip result.embl
\ No newline at end of file
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment