Results for "short reads mapping"
Bio-Scripts
➜ BorisTrinityAssembly /home/urbe/...--assembly is given) 2. read mapping based (if --left and --righ...--left= Left reads file(s) in FASTQ format, comm...--right= Right reads file(s) in FASTQ format,...NFO] 2018-07-13 14:54:34 : No reads provided, skipping read diagnos...2137 days ago
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...] Options...Resume an interupted assembly -h / --help Print short h...1748 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.git...[-v VERBOSITY] [-t THREADS] [-b BARCODE_DIR]..._THRESHOLD] [--check_reads CHECK_READS] [--scoring_schem...adapters found at the ends of reads (...2120 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/bro...n the input SAM/BAM CountReads...Step 2: Aligns reads to the microbe reference...---------------------------- Short Variant Discovery:...nt calling and genotyping for short v...
2089 days ago
Generate simulated polyploid genome !
#Generate 3% divergence msbar -point 4 -count 16558 toy.fasta > toyheterozygous3percent.fasta #Cat both fi...ta > toyheterozygous3percent.fasta #generated 50X of Illumina paired-end reads sim_reads -...2067 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git f...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....
2048 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
1848 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
1739 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### convertin..._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 rows...1617 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fastq-dum...format when aligning. wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/reads/B...1573 days ago
