Results for "long reads"
Bio-Scripts
...naAdapters (Picard) Reads a SAM or BAM file and rewrit...ses in the input SAM/BAM CountReads...sequence of read pairs FilterLongReadAlignmentsSAMSpark...Step 2: Aligns reads to the microbe reference...2087 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous...sta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads sim_reads --depth 50 toyheterozygous3pe...2065 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://gith...fasta greg200k-sv2.2/ref2.fasta greg200k-sv2.2/subreads1.bam 12 18.6M 12 2480k...0 0:00:36 0:00:04 0:00:32 517kgreg200k-sv2.2/subreads1.bam.pbi greg200k-sv2.2/subr...
2046 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
1845 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
1737 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...1614 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ forma...format when aligning. wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/reads/ByRun/sra/SRR/SRR177/SRR17704...1571 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \...#alignment with bwa: bwa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "align using so many threads" and also "give the reads the...n to BAM: samtools view -b - --- this reads SAM from stdin (the - specifi...1571 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads/MitoHunter/minidot/bin$ sudo R [sudo] password for.... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep ch...yes checking whether the C++ compiler supports the long...1562 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioPr...d -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data fo...ll.bam # Reverting the process is to extract reads, tagged with readgroups to pa...1554 days ago
