How quickly can an SRA submission proceed directly from S3
How long would 10TB of RNA-Seq data take to submit to NCBI SRA if it's already in AWS S3?
• 1,661 views
•
link
written
by
Jeremy Leipzig
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Converting SRA Data to FASTQ and Saving Directly to S3
written by Soohyun •
-
Fetch Fastq files directly for SRA data
written by Chintan •
-
bioinformatics pipelines on GCP or AWS
written by Bogdan
-
GEO submission when I have raw data in SRA
written by fifty_fifty •
-
How to download NCBI fastq data to local machine where access type is "Use Cloud Data Delivery"
written by daewowo •
-
RNA seq data analysis
written by arinataj1396 •
-
NCBI SRA AWS AMI
written by noodle
-
Tutorial: NCBI submissions: SRA and TSA
written by saraoppenheim •
-
Forum: What server do you use?
written by caggtaagtat
-
Which repository is more appropriate to submit for cancer cell line (bulk) RNA-seq data ?
written by arta
Have you already got in touch with SRA help desk, if you are truly planning to upload that much data? They can probably suggest efficient/non-standard way.
They should post here then. Isn't the point of biostars to disseminate this type of siloed knowledge?
Need to upload several TB of data is uncommon so while someone who has done this in the past may post you would save time by proactively contacting SRA help desk. While I see some NCBI folks answer questions on biostars I don't think I have ever seen anyone from SRA team here.
If you do get generally usable info please post that. My guess is solutions at this scale may be tailored for specific situations.
My primary concern here is how to upload the metadata and processed files matched the actual fastq files. SRA can use Aspera so for the fastq files it's probably just go and wait. This terrible metadata spreadsheet from GEO is already a pita for a few dozen samples. Leave alone hundreds or thousands.
I'm not sure Aspera is necessary for an S3-to-S3 transfer