Results for "NZ"
Bio-Scripts
Extract ids from file with perl
...#Open and Read a file sub read_fh { my $filename = shift @_; my $filehandle; if ($filename =~ /gz$/) { open $filehandle, "gunzip -dc $filename |" or die $!;...2656 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {pri...2579 days ago
Download the gff files from NCBI using bash script/command
..."GFF$filename" cd "GFF$filename" # take action on each file. $f store current file name head -n 4 $f > $f.head wget --input $f.head gunzip *.gz #cat $f cd .. d...2571 days ago
- zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc
2258 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...ces, \@allIds; } sub read_fh { my $filename = shift @_; my $filehandle; if ($filename =~ /gz$/) { open $filehandle, "gunzip -dc $filename |" or die $!;...2188 days ago
- ...(Picard) Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. CollectWgsMetricsWithNonZeroCoverage (Picard)(BETA Tool...
2123 days ago
- ...++- themes/fino.zsh-theme | 6 +- themes/funky.zsh-theme | 4 +- themes/gnzh.zsh-theme...
2122 days ago
Installing pb-assembly on Linux !
...fc_graph_to_utgs fc-query fc_unzip_gen_gfa_v1.py fc_coords2hp...fc-list fc_quiver.py fc_unzip.py fc_ctg_link_analysis...2082 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory....
2082 days ago
Installing Platypus on Ubuntu !
...-lpython2.7 -o build/lib.linux-x86_64-2.7/variantcaller.so mkdir -p bin cp src/build/*/*.so bin/ cp src/build/*/python/*.py bin/ (py27) ➜ 3-unzip conda install platypus-vari...2067 days ago
