Results for "B"
Bio-Scripts
Install trimmomatic using Conda !
...20-15ISK:~/Downloads/setu/setu$ conda install -c bioconda trimmomatic Collectin...Extracting Packages certifi-2021.5.30 | 139 KB | ########################...########## | 100% openjdk-8.0.152 | 57.4 MB | #########################...1113 days ago
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1113 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name dpkg -s $name &> /dev/null i...1105 days ago
- conda install -c bioconda megahit Collecting package me...ahit The following packages will be downloaded: package | build --------------------...MB The following NEW packages will be INSTALLED: megahit...
1105 days ago
- conda install -c bioconda kat Collecting packa...The following packages will be downloaded: package...sh-2.2.10 | h6bb024c_1 393 KB biocon...4308_11 jellyfish bioconda/linux-64::jellyfish-2....################# | 100% py-boost-1.73.0 | 204 KB |...
1105 days ago
- conda install -c bioconda odgi Collecting package meta...odgi The following packages will be downloaded: package | build --------------------...Total: 237.6 MB The following NEW packages...
1105 days ago
- conda install -c bioconda seqwish Collecting package m...wish The following packages will be downloaded: package | build --------------------...MB The following NEW packages will be INSTALLED: seqwish...
1105 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_...FS= read -r my_file do filename=$(basename "$my_file") basename=$(basename "$my_file"...fastq_small/$filename > results/sam/$basename.aligned.sam samtools...s.fasta results/bam/$basename.sorted.bam bcftools call --ploidy 1...1104 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
Commandline to Extract a list of specific read IDs from a bam file
#Save all the IDs in IDs.txt file #Run it on BAM file samtools view file.bam | fgrep -w -f IDs.txt1055 days ago
