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YuuMJ 2025-06-01 20:28:06 +08:00
parent 93b01501a8
commit 635a7c5199
1 changed files with 3 additions and 7 deletions
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10
3_decontamination/4_Sacc_cerevisiae_dec_cov1_ymj.pbs
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@ -9,12 +9,8 @@ cd /home/Data_01/yizhenzhen06/public_share/Saccharomyces_cerevisiae_DNA/3_decont
echo Start Time is `date` echo Start Time is `date`
blastn -db /home/Data_01/share_databases/human_genome_new/GCF_000001405.39_GRCh38.p13_rna_db \ seqkit seq -n -i ../2_assembly/spades/scaffolds.fasta > 4_Sacc_cerevisiae_dec_all.txt
-query 2_Sacc_cerevisiae_dec_bac_hum.fasta \ awk '{if($1~"_0.")print$1}' 4_Sacc_cerevisiae_dec_all.txt > 4_Sacc_cerevisiae_dec_all_cov1.id
-out 3_Sacc_cerevisiae_dec_bac_hum_geno_rna.tab \ seqkit grep -v -f 4_Sacc_cerevisiae_dec_all_cov1.id 4_Sacc_cerevisiae_dec_all.fasta > 4_Sacc_cerevisiae_dec_all_cov1.fasta
-outfmt "6 qseqid qlen sseqid slen pident qcovs qstart qend sstart send mismatch gapopen evalue bitscore" \
-evalue 1e-5 -max_target_seqs 1 -num_threads 48
sed -i '1i\tquery ID\tquery sequence length\tsubject ID\tsubject qequence length\tpercent identities\tcoverage\tqstart\tqend\tsstart\tsend\tmismatch\tgapopen\tevalue\tbitscores ' 3_Sacc_cerevisiae_dec_bac_hum_geno_rna.tab
echo End Time is `date` echo End Time is `date`