Results for "bedtools"
Bio-Scripts
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-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc2204 days ago
Installing pb-assembly on Linux !
...bcftools: 1.9-h4da6232_0 bioconda bedtools: 2.27.1-he9418...##########################################| Time: 0:00:00 3.76 MB/s bedtools-2.27. 100% |#################...2029 days ago
Setting up falconUnzip conda environments for genome assembly !
...ge avro-python2: 1.8.2-py_1 bioconda bcftools: 1.9-h4da6232_0 bioconda bedtools: 2.27.1-he9418...1984 days ago
Bash command to install GATK, Bedtools and SnpEff !
...g transaction: done (my_GATK) [wsu29@bladeamd-2 tmp]$ conda install bedtools Collecting package metadata...rkshop/wsu29/anaconda3/envs/my_GATK added / updated specs: - bedtools The following packages w...1550 days ago
- (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 --->...
1437 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1360 days ago
Bash script to extract intronic fragments !
...he genic region, we have the intronic region. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort | bedtools subtract -a stdin -b my_exon....1360 days ago
Bash script to get intergenic region from genome files !
...p/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="gene" {print $1,$4-1,$5}' | bedtools sort -g xxx.chrom.sizes | bedtools complement -i stdin -g xxx.ch...1360 days ago
- (JitMetaENV) ➜ assembly conda install -c bioconda prokka Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen sol...
1210 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
991 days ago
