Results for "reads"

Bio-Scripts

  • Estimate Genome Size

    # Count k-mer occurrence using Jellyfish 2.2.6 jellyfish count -t 8 -C -m 19 -s 5G -o 19mer_out --min-qual-char=? sread_1.fastq sread_2.fastq # points for a histogram jellyfish histo -o 19mer_out.histo 19mer_out #Plot results using R ##load the data into dataframe19 dataframe19

    2226 days ago

  • Perl script to check fastq reads qualities !

    #!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!def...

    2116 days ago

  • Coverage / Depth of reads !

    # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_DEPTH}" '$4>=X' | wc -l 328...

    2172 days ago

  • Perl subroutine to read genome/reads fasta file !

    sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/...

    2095 days ago

  • Running Trinity on RNA-seq !

    ...building a k-mer catalog from reads) -- ------------------------..._normalization/tmp_normalized_reads Normalization complete....6.6/trinity_out_dir/chrysalis/readsToComponents.out > /home/urbe/...6/trinity_out_dir/partitioned_reads.files.list.ok Monday, July 9...

    2089 days ago

  • Fastq-dump for SRA download

    ...split into individual reads --split-spot...Split spots into individual reads Full Spot Filters...ference Filters for individual reads Applied only with --spl...reads and above are ignored. -G...

    2088 days ago

  • Long reads mapper bash script !

    #!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2 ref.fa reads.fa/fq 48 ont echo -e "This i...$bwaMemLoc mem $refFasta $longReads -t $thread > $fileName.out.sa...pping with $toolName" if [ $readsType == "ont" ]; then $n...

    2085 days ago

  • Running Transrate !

    ...comma-separated --left= Left reads file(s) in FASTQ format, comma-separated --right= Right reads file(s) in FASTQ format,...n 13 seconds [ INFO] 2018-07-13 14:54:34 : No reads provided, skipping read diagn...

    2085 days ago

  • Installing Porechop on Ubuntu !

    ...stq.gz}] [-v VERBOSITY] [-t THREADS] [-b BARCODE_DIR]...d ADAPTER_THRESHOLD] [--check_reads CHECK_READS] [--scoring_schem...adapters found at the ends of reads (default: 2) --end_thresho...

    2068 days ago