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Commit 5a3aa67f authored by Niko (Nikolaos) Papadopoulos's avatar Niko (Nikolaos) Papadopoulos
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now renaming pseudochromosomes appropriately

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08-submission/gff-01-compose_gff.sh
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...@@ -19,6 +19,14 @@ cd $RESULT || exit ...@@ -19,6 +19,14 @@ cd $RESULT || exit
# merge the GFF3 files # merge the GFF3 files
cat $ISOSEQ $BRAKER_R1 $BRAKER_R2 $DENOVO $TRNASCAN > merged.gff3 cat $ISOSEQ $BRAKER_R1 $BRAKER_R2 $DENOVO $TRNASCAN > merged.gff3
# rename pseudochromosomes 54-59 to 52-57 to reflect decontamination
sed -i 's/pseudochrom_54/pseudochrom_52/g' merged.gff3
sed -i 's/pseudochrom_55/pseudochrom_53/g' merged.gff3
sed -i 's/pseudochrom_56/pseudochrom_54/g' merged.gff3
sed -i 's/pseudochrom_57/pseudochrom_55/g' merged.gff3
sed -i 's/pseudochrom_58/pseudochrom_56/g' merged.gff3
sed -i 's/pseudochrom_59/pseudochrom_57/g' merged.gff3
# sort the GFF3 file # sort the GFF3 file
module load genometools/ module load genometools/
gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3 gt gff3 -tidy -retainids -o merged_sorted.gff3 -force merged.gff3
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