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added question 6

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nicolas-zimmermann 2019-10-24 15:23:46 +02:00
parent 82e27ebc44
commit c1f3f77edf
1 changed files with 3 additions and 3 deletions
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wgs.sh
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@ -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