Download a fastq file

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. The files are all gzipped compressed and the format looks like this, with a four-line repeating pattern ERR What are your filename conventions?

Are there any statistics about how much sequence data is in IGSR? It is a commercial high speed file transfer software produced by IBM. Many sites can transfer data at Mbps. At last, please try fastq-dump and sam-dump in sratoolkit. If the connection of fastq-dump is unstable, I would suggest the wonderdump script in Biostar Handbook. The SRA runs e. SRR correspond to the actual sequencing files that we want to download in order to access the raw data.

This means that the lab had deposited multiple FASTQ files for one sample and did not bother to concatenate them together prior to deposition. You can get more details about how each sample was prepared clicking on the GSM identifier in the Samples section from the first image e. This will take you to the sample description page. I have summarized the different identifiers for GSE in the following table:.

But what is a. If you are using a Linux platform, you can type: apt install sra-toolkit in your command line to install the toolkit. The file SRR The underscore and other special characters e. If there are potential problems with the Sample ID, context-sensitive warnings are shown below the table in the left corner of the window.

Downloading FASTQs and metadata with default settings would result in assembling multiple SRA runs of the same SRA experiment together once a pipeline with default file naming parameters would be started.

Similar, if there would be SRA samples with the same Strain Name also those reads would assemble wrongly together.