From c1f3f77edf25c8f4e6b418032416507c90daa2c3 Mon Sep 17 00:00:00 2001 From: nicolas-zimmermann Date: Thu, 24 Oct 2019 15:23:46 +0200 Subject: [PATCH] added question 6 --- wgs.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/wgs.sh b/wgs.sh index 245793f..67b588c 100644 --- a/wgs.sh +++ b/wgs.sh @@ -28,12 +28,12 @@ soft/megahit --k-list 21 --mem-flag 0 -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -o # Question 4 -soft/prodigal -i contigs/final.contigs.fa -d genes.fna +soft/prodigal -i contigs/final.contigs.fa -d results/genes.fna # Question 5 -sed "s:>:*\n>:g" genes.fna | sed -n "/partial=00/,/*/p"|grep -v "*" > genes_full.fna +sed "s:>:*\n>:g" results/genes.fna | sed -n "/partial=00/,/*/p"|grep -v "*" > results/genes_full.fna # Question 6 - +blastn -query results/genes_full.fna -db databases/resfinder.fna -perc_identity 0.8 -qcov_hsp_perc 0.8 -evalue 1e-3 -outfmt 6 -out results/annoted_genes.dat