Results for "NT"
Bio-Scripts
conda install -c bioconda megahit Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3/envs/ added...1105 days ago
- ...a kat Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen s...ng with flexible solve. Solving environment: failed with repodata from cu...done ## Package Plan ## environment location: /home/anaconda3/env...
1105 days ago
- conda install -c bioconda odgi Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3/envs/ added /...
1105 days ago
- conda install -c bioconda seqwish Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/anaconda3/envs/jitENV...
1105 days ago
Corona variant calling steps !
...-c results/bcf/$basename.vcf > results/bcf/$basename.vcf.gz tabix -p vcf results/bcf/$basename.vcf.gz done mkdir "Variant_Results" cp -r results/bcf/*.vcf Variant_Results/ rem mkdir "Varian...1103 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
1055 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1055 days ago
- (JitMetaENV) ➜ test_phase_assebly conda install -c bioconda bwise Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location:...
1048 days ago
Commandline for paired end reads simulation with BBMap !
...ds.sh ref=mixed.fa out=reads_BBMAP250.fq paired interleaved reads=100k length=250...-ea -Xmx162129m -cp /home/urbe/Tools/bbmap/current/ align2.RandomReads3 build=1...1, ref=mixed.fa, out=reads_BBMAP250.fq, paired, interleaved, reads=100k, length=2...1048 days ago
Commands to transfer files and folder in docker !
#To copy files between host machine and container (execute the commands on host, not inside container): $ docker cp FILE_OR_FOLDER_ON_HOST CONTAINER_ID:/CONTAINER_DIRECTORY #or $ docker cp CONTAINER_ID:FILE_OR_FOLDER_IN_CONTAINER HOST_DIRECTORY1044 days ago
