Results for "FASTQ"
Bio-Scripts
(JitMetaENV) ➜ fastQC_out trimmomatic SE -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLE...TrimmomaticSE: Started with arguments: -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 T...1213 days ago
Download minikraken database !
...kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201904_UPDATE --fastq-input --report evol1 --gzip-compressed --paired ../mappings/evol1.sorted.unmapped.R1.fastq.gz ../mappings/evol1.sorted.u...1211 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
993 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysam...973 days ago
Trim the reads in loop using Trimmomatic !
for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${ba...un.trim.fastq.gz \ ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz...951 days ago
- ...overage=30 paired=t maxinsert=550 mininsert=450 \ out1=illumina1.fastq.gz out2=illumina2.fastq.gz > random_reads_illumina.lo...t \ minlength=1000 midlength=20000 maxlength=30000 \ out=pacbio.fastq.gz > random_reads_pacbio.log...
925 days ago
Bash script to simulate a genome !
...genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslash=t \ coverage=30 paired=t maxinsert=550 mininsert=450 \ out1=illumina1.fastq.gz out2=illumina2.fastq.gz > random_reads_illumina.lo...914 days ago
Rules to run fastp / Snakemake !
...nput: fwd=INPUT + "/{sample}-read_1.fq", rev=INPUT + "/{sample}-read_2.fq" output: fwd=RESULTS + "/fastq_trimmed/{sample}.1.trimmed.fastq", rev=RESULTS + "/fa...898 days ago
Bash command to count reads in fastq file !
#ref fastq file #ref1_1.fq) echo $(( $(wc -l788 days ago
Raku script to find SSRs in fastq file !
...} } } return @ssrs; } sub process-fastq-file(Str $filename) { my...} } } $fh.close; } # Replace 'your_fastq_file.fastq' with the path to...108 days ago
