Results for "FASTQ"
Bio-Scripts
Installing Porechop on Ubuntu !
.../home/urbe/anaconda3/bin ➜ Porechop git:(master) porechop -h usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]...2103 days ago
- ...0_Adineta_Nature_and_Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R1.fastq /home/urbe/DATA/OriginalReads...0_Adineta_Nature_and_Habrotrocha.160226.HiSeq2000.FCB.lane1.gcap_dev.R2.fastq out.smaltmap.bam echo " sma...
2096 days ago
- ...e for each read in an Illumina lane. IlluminaBasecallsToFastq (Picard) Generate FASTQ file(s) from Illumina basecal...Converts a BAM file into a BFQ (binary fastq formatted) file BaseReca...
2072 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....
2031 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
1831 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
1722 days ago
Bash script to download SRA file !
...se the sratoolkit to directly pull the sequence data (in paired FASTQ format) from the archive. fastq-dump is in the SRA toolkit. I...irectly downloading data from a particular sequencing run ID fastq-dump --split-files SRR1770413...1556 days ago
Bash script to alignment of short reads against reference genome !
...' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.fastq.gz \ | samtools view -b...2 and the sample name K12" #reference and FASTQs E.coli_K12_MG1655.fa SRR1770...4' \ E.coli_K12_MG1655.fa SRR341549_1.fastq.gz SRR341549_2.fastq.gz \...1556 days ago
To convert just one specific read group to fastq
...SRR data for each cat selected.txt | parallel fastq-dump -O reads -X 1000 --split...h SAMPLE. cat selected.txt | parallel "picard FastqToSam F1=reads/{}_1.fastq F2=r...ls view -r GROUP-SRR1972919 all.bam | samtools fastq -t -1 all_SRR1972919_1.fq -2...1539 days ago
- #This method can be applied directly to FASTA or a FASTQ file, compressed or uncompressed files. Seqtk is a fast and lightweight tool for processing biological data (FASTA/FASTQ). if you have a list of ident...
1399 days ago
