Questions tagged [sra]

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Downloading multiple SRA files as FASTQ files using SRA Toolkit

I was able to download all of the SRA files for a specific bioproject using the command: prefetch -O output_directory --option-file SRR_Acc_List.txt I then tried ...
Lucy's user avatar
  • 13
0 votes
1 answer
78 views

How to download Sequencing data on Windows using SRA toolkit?

I have downloaded and installed the SRA toolkit, but there seems to be no online material on how to download SRR files using the SRA toolkit on Windows. All online materials are Ubuntu or Linux based. ...
Sanjukta Ghosh's user avatar
2 votes
0 answers
79 views

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
1 vote
0 answers
43 views

Journal article reference for Illumina's "near monopoly" [closed]

Apologies if the question is out of the scope of the bioinformatics SE. Please feel free to close it if it is the case. Recently, I have been going into a rabbit hole of papers that discuss the ...
Laura's user avatar
  • 11
2 votes
2 answers
333 views

ZIP the fasterq-dump files in loop

I want to zip the files generated by fasterq-dump simultaneously as they are generated. The code that I tried is this. ...
Shradha Sharma's user avatar
0 votes
0 answers
31 views

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
2 votes
0 answers
96 views

Problem with nextflow -resume and path.fromSRA

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

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: ...
rimo's user avatar
  • 963
3 votes
2 answers
557 views

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 ...
Kamil S Jaron's user avatar
2 votes
1 answer
158 views

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 https://trace.ncbi.nlm.nih.gov/...
Dougnukem's user avatar
  • 121
1 vote
0 answers
274 views

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
  • 909
4 votes
1 answer
677 views

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: ...
An Ignorant Wanderer's user avatar