Download fastq files

Because of this, users with data located on GPFS filesystems will see significant slowdowns in their jobs. 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. The files which do not have a number in their name are singled ended reads, this can be for two reasons, some sequencing early in the project was singled ended, also, as we filter our fastq files as described in our README if one of a pair of reads gets rejected the other read gets placed in the single file.

When a individual has many files with different run accessions e. This can either be for the same experiment, some centres used multiplexing to have better control over their coverage levels for the low coverage sequencing, or because it was sequenced using different protocols or on different platforms.

For a full description of the sequencing conducted for the project please look at our sequence. You can search for individuals, populations and data collections, and filter the files by data type and technologies.

This will give you locations of the files, which you can use to download directly, or to export a list to use with a download manager. Is there a command line to check the integrity of the data? If we previously downloaded the same data, is it a smart move to clean the cache after we deleted those files? WiFi connection for that much of data sounds like a bad idea but if you have great upstream connectivity e. Just to add, there is also this great video from Babrahan Bioinformatics that cover some of the topics mentioned in this tutorial:.

Just need a list of IDs and whack it into:. Easily parallelized in an HPC environment and also snags the metadata, optionally formatting it into samplesheets for downstream nf-core pipelines if wanted. Instructions can be found here. You can download ascp as part of aspera here :. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown.

Featured on Meta. Reducing the weight of our footer. Now live: A fully responsive profile. Related 5. Hot Network Questions. We observe that two fastq files have been extracted from SRR This is because the original data was produced from paired-end sequencing, which usually has both a Read1 file and Read2 file. I typically use the settings provided above for fastq-dump as my default settings.

Since there are lots of SRA files associated with our samples, it would take a long time to manually run prefetch and fastq-dump for all the files. To automate this process, I wrote a small script in python to first download each SRA file using prefetch and then run fastq-dump. I would advise against it, since I have found this method to be much slower than first running prefetch and then fastq-dump on the pre-downloaded SRA files.

In comparison, running fastq-dump without pre-downloading the files for the same SRA ID took a total time of 77 minutes 34 seconds!