Download SRA file

If not, go to SRA database. First Choice — Aspera Connect. 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. Warning : Try not to use wget or curl to download, it might cause incompletion in downloaded sra files. Firstly, go to Aspera Connect , choose the linux version and copy link address. Let's actually get some ATAC-seq reads. To automatically download sample metadata and generate configuration files that will allow us to convert the.

Next we're going to convert those downloaded. If you haven't installed looper , do that now before moving forward see looper docs. Looper requires a few variables and configuration files to work for a specific user. For more detailed information regarding this file, check out the looper docs. The looper environment configuration file points to submission template s in order to know how to run a sample or series of samples. We're going to simply setup a local template for the purposes of this tutorial.

You can also easily create templates for cluster or container use as well! We also need to create additional environment variables to help point looper to where we want to download and convert our. You may either set the environment variables or you simply hard code the necessary locations in the configuration file.