Questions tagged [sra]
The sra tag has no usage guidance.
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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 ...
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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 ...
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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.
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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?
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Problem with nextflow -resume and path.fromSRA
I have a problem with nextflow -resume
Here is my script :
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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:
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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 ...
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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/...
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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 ...
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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:
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