Open ruicatxiao opened 3 years ago
wget https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR8154672/SRR8154672.1 fasterq-dump -e 8 -v --split-files ./SRR8154672.1 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz
awk -F '\t' -v OFS='\t' '$3 ~ /gene/' k12.gff > geneonlygenome.gff awk -F '\t' -v OFS='\t' '{new_var="NAME="substr($9,4,10); print $1, $6, $3, $4, $5, $6, $7, $8, new_var}' geneonlygenome.gff > geneonlygenome1.gff
sort -k1,1 -k4,4n geneonlygenome1.gff > geneonlygenome2.gff cat gffheader.txt geneonlygenome2.gff > forplottinggene.gff
trim_galore --cores 6 --paired --fastqc SRR8154672.1_1.fastq SRR8154672.1_2.fastq
methylpy build-reference --input-files genome/k12.fa \ --output-prefix k12 \ --num-procs 4
methylpy paired-end-pipeline \ --read1-files SRR8154672.1_1_val_1.fq \ --read2-files SRR8154672.1_2_val_2.fq --sample k12_1 \ --forward-ref k12_f \ --reverse-ref k12_r \ --ref-fasta k12.fa --num-procs 8 \ --trim-reads False \ --min-cov 3 \ --merge-by-max-mapq True --remove-clonal True \ --path-to-picard "$EBROOTPICARD/"
perl formetaplot.pl -gff forplottinggene.gff -allc allc_mCG.tsv -o cp_mcg
wget https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-1/SRR8154672/SRR8154672.1 fasterq-dump -e 8 -v --split-files ./SRR8154672.1 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.gff.gz
awk -F '\t' -v OFS='\t' '$3 ~ /gene/' k12.gff > geneonlygenome.gff awk -F '\t' -v OFS='\t' '{new_var="NAME="substr($9,4,10); print $1, $6, $3, $4, $5, $6, $7, $8, new_var}' geneonlygenome.gff > geneonlygenome1.gff
sort -k1,1 -k4,4n geneonlygenome1.gff > geneonlygenome2.gff cat gffheader.txt geneonlygenome2.gff > forplottinggene.gff
trim_galore --cores 6 --paired --fastqc SRR8154672.1_1.fastq SRR8154672.1_2.fastq
methylpy build-reference --input-files genome/k12.fa \ --output-prefix k12 \ --num-procs 4
methylpy paired-end-pipeline \ --read1-files SRR8154672.1_1_val_1.fq \ --read2-files SRR8154672.1_2_val_2.fq --sample k12_1 \ --forward-ref k12_f \ --reverse-ref k12_r \ --ref-fasta k12.fa --num-procs 8 \ --trim-reads False \ --min-cov 3 \ --merge-by-max-mapq True --remove-clonal True \ --path-to-picard "$EBROOTPICARD/"
perl formetaplot.pl -gff forplottinggene.gff -allc allc_mCG.tsv -o cp_mcg