Several examples of setting the file path parameters: 1. Single end fastq files -f file1.fq,file2.fq -q 2. Single end fasta files -f file1.fa,file2.fa,file3.fa 3. Paired-end fastq files --p1 file1_1.fq,file2_1.fq --p2 file1_2.fq,file2_2.fq…
Contribute to stormlovetao/xQTLimp development by creating an account on GitHub. By default, peddy uses hg19/GRCh37. It can be forced to use sites for hg38 by passing --sites hg38. To create custom sites, have a look at the sites files included with peddy along with the corresponding .bin.gz which is just the raw binary… Scripts for downloading reference genomes and annotations - gwcbi/cbi_reference_genomes The file must have the original format provided by gencode, gzipped files are not supported. The code inputs a single wiggle file and generates a single binary power Fasta file. Therefore, it is well suited for parallelization. Dolfin User Manual | manualzz.com The NIH HPC staff maintains several hundred scientific programs, packages and databases for our users. Below is a list of system-installed software available on Biowulf and Helix.
-> angsd version: 0.910-14-g5e2711f (htslib: 1.2.1-252-ga2656aa) build(Dec 4 2015 10:40:24) -> Analysis helpbox/synopsis information: -> Command: ./angsd -bam -> angsd version: 0.910-14-g5e2711f (htslib: 1.2.1-252-ga2656aa) build(Dec 4 2015… T-Gene's only other required input is a gene annotation file, and computes a statistical, distance-based score for each potential regulatory link between a locus in the BED file and a transcription start site (TSS) of a transcript in the… After the update, this refGene.txt.gz file will be processed by AnnotSV during the first run (it will take longer than usual AnnotSV runtime). reference sequences and annotation files for commonly analyzed organisms - igordot/reference-genomes Aprenda Mysql by Oreilly Introd - Free ebook download as PDF File (.pdf), Text File (.txt) or read book online for free. tutor mysql
This will generate a file with a ".fai" extension which must be in the same directory as the Fasta file; thus it is necessary that the directory containing the file be writable. CAVA v1.2.0 documentation Contents 1 Introduction Installation Running CAVA Configuration FILE Input FILE Implementation of structural variant finding algorithm arriba by Sebastian Uhrig - BD2KGenomics/dockstore_tool_arriba -o * output directory -r * reference genome -v * VCF file or directory --gz flag denoting VCF files are gzipped --rnaedit ** flag to N-mask rna editing sites -e ** file containing RNA editing sites, can be downloaded from Radar (http… C++ htslib/bwa-mem/fermi interface for interrogating sequence data - walaj/SeqLib
-o * output directory -r * reference genome -v * VCF file or directory --gz flag denoting VCF files are gzipped --rnaedit ** flag to N-mask rna editing sites -e ** file containing RNA editing sites, can be downloaded from Radar (http… C++ htslib/bwa-mem/fermi interface for interrogating sequence data - walaj/SeqLib hg19.bowtie2_index/hg19_trans/hg19_known_ensemble_trans.* How to get: download from (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) or follow instructions provided by bowtie2. Runs STARFusion and arriba. Contribute to BD2KGenomics/dockstore_workflow_fusion development by creating an account on GitHub. python radia.py patientId chrom -n normalDnaBamFilename.bam -t tumorDnaBamFilename.bam -r tumorRnaBamFilename.bam -f hg19.fa --rnaTumorUseChr --rnaTumorFasta=hg19_w_chr_prefix.fa -o /radia/raw/patientId_chr1.vcf.gz -i hg19 -u http://url_to… Contribute to mcfrith/tandem-genotypes development by creating an account on GitHub.
hg19/UCSC-style chromosome naming convention ("chr1"); b37/1000 Genomes-style chromosome To create a reference, run the longranger mkref command on your FASTA file. tracks in the Loupe genome browser, download our gene annotations file into your reference. The file must be compressed in gzip format.
