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NCBI-Hackathons / Got_Plasmid

Retreive and visualize plasmid sequences from SRA and Next Generation Sequencing data.
MIT License
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Got plasmids? #3

Open DCGenomics opened 6 years ago

DCGenomics commented 6 years ago

https://www.ncbi.nlm.nih.gov/genome/plasmids/154?

awk -F"\t" '{print $7}' genomes_plasmids.txt -- for genbank $7, for refseq $6

esearch -db nucleotide -query CP007178 | efetch -format fasta > test.fasta

makeblastdb -dbtype nucl -in test.fasta

DCGenomics commented 6 years ago

The objective would be to generate a matrix for datasets and plasmids?

Rickcopin commented 6 years ago

magicblast -db test.fasta -sra SRR6227128 -perc_identity 90 > testout.foo &

Rickcopin commented 6 years ago

magicblast -db test.fasta -sra SRR6227128 -no_unaligned -splice F -score 50 -outfmt tabular

Rickcopin commented 6 years ago

blastn -db S_aureus_gapless.fasta -query /panfs/pan1.be-md.ncbi.nlm.nih.gov/product_manager_research_projects/richard_copin/contigs/matching_contigs_AB254848.fasta -parse_deflines -evalue .0000000001 -outfmt 6 -out sample_contigs_into_gapless_S_aureus_genomes.blastout

Rickcopin commented 6 years ago

genome_getter.sh

!/bin/bash

for i in cat S_aureus_gapless_assemblies; do wget esearch -db assembly -query "$i" | efetch -format docsum | xtract -pattern DocumentSummary -element FtpPath_GenBank | awk -F"/" '{print $0"/"$NF"_genomic.fna.gz"}'; done

gunzip *.gz