Our sequence files are distributed in gzipped fastq format. Our files are named with the SRA run accession E? All the reads in the file also hold this name. If there is also a file with no number it is name this represents the fragments where the other end failed qc.
Our variant files are distributed in vcf format , a format initially designed for the Genomes Project which has seen wider community adoption. This name starts with the population that the variants were discovered in, if ALL is specifed it means all the individuals available at that date were used. Then the region covered by the call set, this can be a chromosome, wgs which means the file contains at least all the autosomes or wex this represents the whole exome and a description of how the call set was produced or who produced it, the date matches the sequence and alignment freezes used to generate the variant call set.
Next a field which describes what type of variant the file contains, then the analysis group used to generate the variant calls, this should be low coverage, exome or integrated and finally we have either sites or genotypes. A sites file just contains the first eight columns of the vcf format and the genotypes files contain individual genotype data as well. Release directories should also contain panel files which also describe what individuals the variants have genotypes for and what populations those individuals are from.
Format We use Sanger style phred scaled quality encoding. If this approach fails for whatever reasons, then the SRA toolkit is also used to retrieve and download the FASTQ file which takes normally longer than the direct download. A list of accessions for all available SRA sequences of a certain species, can be downloaded from the SRA website using the following steps:. See more details at NCBI Result table with meta-data for all runs that were found for the given accessions The found metadata for the given accessions are shown in a table, where each row represents one SRA run.
Four different filters are available: The runs can be filtered by a sequencer vendor, e. The runs can be filtered by the sequencing protocol, i. SRA samples can be filtered for strain name: if selected, the table shows only run s of the SRA sample with largest experiment, if multiple SRA samples are found with the same strain name. See the section on using local disk in the Biowulf User Guide. Here is a sample file that downloads SRA data using fasterq-dump.
For example, to allocate GB of scratch space and 4GB of memory:. NCBI's database of Genotypes and Phenotypes dbGaP was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.
Most dbGaP data is controlled-access. Documentation for downloading dbGap data. If you are having problems with dbGaP downloads, please try this test download. This is to confirm whether it is a general problem, or specific to your configuration, or specific to the accessions you are trying to download.
Changes with SRAToolkit v2. The hisat program can automatically download SRA data as needed.
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