Skip to main content

Questions tagged [sra]

The tag has no usage guidance.

5 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
2 votes
0 answers

Get SRR numbers from a GSE number

I'm trying to programmatically download files from SRA (with prefetch in sra-tools) starting from a GSE number, using Python. There is an explanation for using entrez-direct on the CLI, using esearch ...
Freek's user avatar
  • 563
2 votes
0 answers

Problem with nextflow -resume and path.fromSRA

I have a problem with nextflow -resume Here is my script : ...
eva fonta's user avatar
2 votes
1 answer

How to determine NCBI's SRS google cloud bucket or AWS bucket

It appears that AWS and GCP host SRA data and it's beneficial to grab the data from that source when running on GCP for example. Given an SRR accession like SRR1929796
Dougnukem's user avatar
  • 121
1 vote
0 answers

How to use SRA Toolkit to blast SRA accessions?

I'm trying to look for a gene in a group of SRA files. Web BLAST can't cope with them, so I assume they're too large. I've tried tblastn_vdb from the SRA toolkit, as follows. It had previously worked ...
Laura's user avatar
  • 907
0 votes
0 answers

How to access specific SRA sequences within an SRP file?

How do you get a specific 100 SRA sequences from a Bioproject which contains 400 runs, when you don't need all of them?
K_081's user avatar
  • 149