Questions tagged [sra]

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Problem with nextflow -resume and path.fromSRA

I have a problem with nextflow -resume Here is my script : ...
1 vote
1 answer

Fixing FASTA file for Local BLAST Database

I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format. Each individual FASTA file looks something like this: ...
  • 453
3 votes
2 answers

What happened to sra ftp server?

My whole (professional) life I am downloading sequences from SRA and ENA databases. Long time ago, I used prefetch from sra-tools, but later I switched to simply using wget from ftp servers of the two ...
0 votes
0 answers

How to download metadata in SRA (i.e., SraRunTable.txt) using Unix commands?

We can obtain metadata (the SraRunTable.txt file) from the webpages in SRA. How to get this file using Unix commands? A potential solution was given in
  • 113
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
  • 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 ...
  • 755
4 votes
1 answer

Programmatically retrieve Metadata from SRA Run Selector

I previously asked a question about how to retrieve the Accession List associated with a SRA project. The answer was: ...