RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon - NCBI-Hackathons/rnaseqview BAM files undergo consensus construction through the workflow illustrated above. Output BAMs are grouped according to type of error suppression (SSCS vs DCS) and whether Singleton Correction (SC) was implemented. Tools to search through the Sequence Read Archive using Xsede's Jetstream - linsalrob/SearchSRA Contribute to fiber-miniapp/ngsa-mini development by creating an account on GitHub. instructions, python and R code for generating lava lamp plots of kmer coverage - wrf/lavaLampPlot ATAC-seq lab for Bioinf525. Contribute to ParkerLab/bioinf525 development by creating an account on GitHub.
Open Science Grid Workflow That Creates Gene Expression Matrices (GEMs) from SRA/Fastq NGS Files - feltus/OSG-GEM
A repository for the Elixir-GR project implemented by HybridStat - hybridstat/elixir-gr-project Contribute to NCBI-Hackathons/Virus_Detection_SRA development by creating an account on GitHub. STAR-HTSeq RNA-seq processing pipeline environment and wrapper script, including SRA query, download, and caching functionality and useful reuse/restart features - hermidalc/rna-seq-star-htseq To use the Aspera service you need to download the Aspera connect software. This provides a bulk download client called ascp. sri = read.csv("SraRunInfo.csv", stringsAsFactors=False) keep = grep("CG8144|Untreated-",sri$LibraryName) sri = sri[keep,] fs = basename(sri$download_path) for(i in 1:nrow(sri)) download.file(sri$download_path[i], fs[i]) names(sri) [1] "Run… Opdownload (.opdownload) – partly complete Opera download
instructions, python and R code for generating lava lamp plots of kmer coverage - wrf/lavaLampPlot
Nextflow pipeline for ChIP-seq analysis. Contribute to Dowell-Lab/ChIP-Flow development by creating an account on GitHub. This repository contains our CellTag CloneHunter R package for clone-calling. - babiddy/CloneHunter SRA Tools. Contribute to ncbi/sra-tools development by creating an account on GitHub. NCBI claims to have fixed the issue but if users encounter errors, we strongly suggest that those working with the data download and realign the fastq files above rather than using the files deposited in the SRA.
The NCBI's Sequence Read Archive (SRA) is the database we will be using for this The SRA does not support direct download of fastq files from its webpage.
ATAC-seq lab for Bioinf525. Contribute to ParkerLab/bioinf525 development by creating an account on GitHub. Contribute to Npsdc/Mapping_alpha development by creating an account on GitHub. For example, you can find the SRA file SRR390728.sra in ~/ncbi/sra and the resource files in ~/ncbi/refseq. Then you can run other SRA tools, e.g. fastq-dump on computing nodes.
It additionally contains pre-processed .bam and .bai files in case you would like to try only Rcount and to skip the download and alignment part of the tutorial (in this case go to section 2.4). Assay for Transposase Accessible Chromatin (ATAC-seq) is an open chromatin profiling assay that is adapted to interrogate chromatin accessibility from small cell numbers. ATAC-seq surmounted a major technical barrier and enabled epigenome…
A repository for the Elixir-GR project implemented by HybridStat - hybridstat/elixir-gr-project
Download and decompress SRA files to FastQ format using the NCBI SRA Toolkit: # Download/decompress reads $ fastq-dump -A SRR972714 # Nuclease S1 12 Jun 2019 Formats of sequencing data files; BAM file; fastq; 454; Illumina The Experiment, Run and Analysis are the SRA objects, and the download Experiment metadata into a tab-delimited text file, edit title values and upload it. 25 Feb 2018 So whenever you access the SRA database, you will have to download sra files, and then convert them into fastq files (often, one would also