Results for "reads"
Bio-Scripts
...MarkIlluminaAdapters (Picard) Reads a SAM or BAM file and rewrite...l) Counts bases in the input SAM/BAM CountReads...rk Step 2: Aligns reads to the microbe reference...2069 days ago
Generate simulated polyploid genome !
...t.fasta #Cat both files cat toy.fasta toymutated3percent.fasta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads sim_reads --depth 50 toyheterozygous3pe...2047 days ago
- ...greg200k-sv2.2/ref1.fasta greg200k-sv2.2/ref2.fasta greg200k-sv2.2/subreads1.bam 12 18.6M 12 2480k...0 0 517k 0 0:00:36 0:00:04 0:00:32 517kgreg200k-sv2.2/subreads1.bam.pbi greg200k-sv2.2/subr...
2028 days ago
- bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam
1828 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1719 days ago
Samtools commands for bioinformatician !
...le into fasta samtools fasta reads_mapped.sam > reads.fasta #..._sej.bam | less ### sort reads by flag specified and show th...sej.bam | less ### count reads (-c) by flag specified samto...le has two columns: QC-passed reads and QC-failed reads # and ro...1597 days ago
Bash script to download SRA file !
...for the first and second mate in each pair. We'll use them in this format when aligning. wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/reads/ByRun/sra/SRR/SRR177/SRR17704...1553 days ago
Bash script to alignment of short reads against reference genome !
...by line: #alignment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "align using so many threads" and also "give the reads the...conversion to BAM: samtools view -b - --- this reads SAM from stdin (the - specifi...1553 days ago
To convert just one specific read group to fastq
..., | grep SRR | head -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data fo...GROUP-SRR1972919 all.bam # Reverting the process is to extract reads, tagged with readgroups to pa...1536 days ago
Perl script to reads and extract webpage contents !
use 5.010; use strict; use warnings; use WWW::Mechanize; my ($url) = @ARGV; die "Usage: $0 URL\n" if not $url; my $w = WWW::Mechanize->new; $w->get($url); say $w->content; #Run #jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com1507 days ago
