Download data from ncbi short read archives

In my case those were already created because the genome were already on NCBI. I just added the identifiers when prompted. If you do not have one, create one. Create a new submission. All your data that is grouped under the same submission will have the same release date.

You can set your data to be released at a particular date. The earliest you can do is the following day at midnight. I am not sure how long you can keep your data private but the refilled release date is set for 1 year from the day you start the submission.

Once your submission is create, you can create a new experiment. The experiments are linked to a sample. You can have multiple experiments link to the same BioSample. For this step you will need:. The name of the platform, alias, title and a BioProject identifier, BioSample identifier. You will also need to specify a name for the library construction, a strategy from a list of predefined terms , Source and Selection method used. Optionally you can add links to other Dbs or websites for the particular experiment.

A pipeline information can also be entered but is not required. Once you have entered the required data, you can save and your experiment will now show up in the submission table.

For HDF5 submission, you need to submit 4 files. I compressed the files using gzip but it did not reduce the file size that much maybe I will skip this next time. I have not submitted any other file format so far.

There are descriptions on the SRA website for what they are expecting for each format or platform. Before you upload the files to the SRA ftp, you will need to enter the file name as well as the MD5 checksum for the file. This is used to make sure the file that they received is the same as the file you are intending on sending. Or I need to do a manual conversion to mysql from json using this API.

I am a programmer at this 3d rendering firm and need to my cousin with this api. Share this post: Twitter Facebook Print Email. Like this: Like Loading Leave a Reply Cancel reply. Loading Comments Email Required Name Required Website. Sorry, your blog cannot share posts by email.