Results for "samtools"
Bio-Scripts
(base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 --->...1438 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen sol...
1211 days ago
Corona variant calling steps !
...em trimmed_fastq_small/$filename > results/sam/$basename.aligned.sam samtools view -S -b results/sam/$basename.aligned.sam > results/bam/$basename.aligned.bam samtools sort -o results/bam/$basename...1041 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
992 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.txt992 days ago
Bash script to simulate a genome !
...nlm.nih.gov/genomes/all/GCA/003/401/745/GCA_003401745.1_ASM340174v1/GCA_003401745.1_ASM340174v1_genomic.fna.gz # Use BCFtools 1.10.2 and SAMtools 1.10 conda activate bcftools...914 days ago
- ..._dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species1.sam samtools sort toy_dataset_mapped_species1.bam -o toy_dataset_mapped_species1_sorted.bam samtools index toy_dataset_mapped_spec...
863 days ago
Extract the mapped and unmapped reads !
PROCESSORS=20 #Single_End_Layout: samtools view --threads $PROCESSORS -b -F 4 in.bam > mapped.bam samtools view --threads $PROCESSORS -b -f 4 in.bam > unmapped.bam #Paired_End_Layout samtools view --threads $PROCESSORS -b...586 days ago
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