Results for "NGS READGROUPS GATK FastQ"
Bio-Scripts
➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3...ted --left= Left reads file(s) in FASTQ format, comma-separated --right= Right reads file(s) in FASTQ format,...2162 days ago
Installing Porechop on Ubuntu !
➜ Tools git:(master) ✗ git clone https://github.com/rrwick/Porechop.g...[--format {auto,fasta,fastq,fasta.gz,fast...default: 16) Barcode binning settings: Control the binning of read...fault: False) Adapter search settings: Control how the program det...2145 days ago
- set -e echo "Running reapr version 1.0.18 pipeline:" e..._Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R1.fastq /home/urbe/DATA/OriginalReads..._Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R2.fastq out.smaltmap.bam echo " sma...
2138 days ago
- jitendra@jitendra-UNLOCK-INSTALL[...s://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip --2018-08-30 11:...ne. IlluminaBasecallsToFastq (Picard) Generate FASTQ file(s) from Illumina baseca...a BAM file. AddOrReplaceReadGroups (Picard) As...
2114 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-sym' already exists and is not an empty directory....
2073 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
1873 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1764 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-dump is in the SRA toolkit. I...a particular sequencing run ID fastq-dump --split-files SRR1770413...ools, so it's necessary to put things into FASTQ for further processi...1598 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \...E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b...he sample name K12" #reference and FASTQs E.coli_K12_MG1655.fa SRR1770...E.coli_K12_MG1655.fa SRR341549_1.fastq.gz SRR341549_2.fastq.gz \...1598 days ago
Bash command to install GATK, Bedtools and SnpEff !
(my_GATK) [wsu29@bladeamd-2 tmp]$ conda install gatk Collecting package metadata...kshop/wsu29/anaconda3/envs/my_GATK added / updated specs:...py38_0 156 KB gatk-3.8 |...:certifi-2019.11.28-py38_0 gatk bioconda/noarch...1594 days ago
