![]() ![]() In the following image the data will be downloaded to /scratch/keeko/prefetchData. Then set the "location of user-repository" to the empty folder you created. ![]() Make sure there is an X by the "Enable Remote Access" option on the MAIN tab, and X by the "enable local file-caching" option in the CACHE tab. This will open a screen where you operate the buttons by pressing the letter highlighted in red, or by pressing the tab-key until the wanted button is reached and then pressing the space- or the enter-key. It is recommended that you download data into your scratch directory since there is plenty of space there. Then create the folder where prefetch will deposit your files. Once you find a dataset you would like to download, search for the "Run number" in the table towards the bottom of the webpage for that dataset. You can search for a dataset using the search bar at the top of the SRA homepage. This program downloads Runs (sequence files in the compressed SRA format) and all additional data necessary to convert the Run from the SRA format to a more commonly used format. You can download SRA data to local directory with the prefetch tool. To use this version, please load the module with The SRA file contains a set of instructions for downloading the sequencing data associated with the SRA ID from NCBI. The last version of this application is at /apps/eb/SRA-Toolkit/2.11.1-centos_linu圆4/ The toolkit works by first using the prefetch command to download the SRA file associated with the specified SRA ID. Download sequence data files using SRA Toolkit SRA Run files hold only sequence data and do not contain any metadata (sample information, etc. Validate the integrity of downloaded SRA data ![]() Output the native VDB format of SRA data.Įncrypt non-SRA dbGaP data ("phenotype data") Generate statistics about SRA data (quality distribution, etc.) To use it, load the sratoolkit module: module load sratoolkit. Generate pileup statistics on aligned SRA dataĭisplay and modify VDB configuration informationĭecrypt non-SRA dbGaP data ("phenotype data")Ĭonvert SRA data into ABI format (csfasta / qual)Ĭonvert SRA data into Illumina native formats (qseq, etc.) The SRA-Toolkit includes the following tools:Īllows command-line downloading of SRA, dbGaP, and ADSP data In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. The Sequence Read Archives (SRA) store raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopores. The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. I was looking for some crab transcriptomic data today and, unable to find any previously assembled transcriptomes, turned to the good ol’ NCBI SRA. ![]()
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