Questions tagged [sratoolkit]

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2 answers
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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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2 votes
1 answer
74 views

How do I set my path for the SRA toolkit under macOS 12.1?

I would like to add the SRA toolkit to my path under macOS 12.1. After downloading the SRA directory, decompressing, and adding to the path, the directory does not seem to be available e.g. I'm ...
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2 votes
1 answer
65 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/...
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  • 121
1 vote
0 answers
147 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 ...
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  • 627
0 votes
1 answer
189 views

Why am I getting empty expression data from GEO?

I am trying to analyze the scRNAseq data from this study. In their Method section they write: The accession number for the RNA and DNaseq data reported in this paper is GEO: GSE116237. When I go ...
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0 votes
3 answers
51 views

Genome QC + Assembly Pipeline semantics

I’m trying to create a pipeline for genome assembly. How best can I “redirect/pipe” from existing fasta files (or files in general) to other steps of the pipeline? I was thinking of going from the SRA ...
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0 votes
1 answer
292 views

Error in if (is.na(sra_acc$run[i])) { : argument is of length zero

I am trying to write a code for importing sra files as fastq files in Rstudio (for obtaining and aligning RNA-seq reads from public repositories). I keep getting "Error in if (is.na(sra_acc$run[i]...
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0 votes
2 answers
127 views

Using variables with fasterq-dump?

I am trying to download multiple fastq files from the SRA NCBI database which, conveniently enough, have their IDs in a range. Building a simple loop doesn't seem to do the trick, as bash appears to ...
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0 votes
1 answer
40 views

How to extract metadata from NCBI's experiment?

I want to extract metadata from experiment SRX1596422. I have sratoolkit and Entrex direct but not sure what line of code to use. Here's the link for the experiment: experiment SRX1596422
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1 vote
1 answer
1k views

How to split FASTQ reads without re-running `fastq-dump`?

I downloaded a few FASTQs from the SRA that were paired-end 76 bp. When I look at the FASTQs, I get something like this: ...
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  • 1,192
0 votes
1 answer
24 views

SRA Toolkit and lebanese data

I am trying to extract data from this: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218 I installed SRA Toolkit, downloaded the SRR6245218 file and executed this: ...
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1 vote
1 answer
57 views

Fastq-dump script download X spots or all

Im trying to write a script where an optional input of -X flag can be used, or if that info is not available download all reads. my script as follow: ...
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0 votes
1 answer
362 views

SRA Toolkit execution problem

I am trying to install SRA Toolkit on MacOS, following all the instructions from NCBI website. It is installed but fastq-dump cannot be executed because "cannot execute binary files". I tried "chmod +...
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2 votes
1 answer
1k views

Fasterq-dump: --split-spot or -concatenate-reads?

After using files that I downloaded from the SRA with fasterq-dump, I realize I am not 100% sure that I have all the data. I noticed in my downstream analysis that I seem to be missing the .1 and .2 ...
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  • 627
6 votes
1 answer
68 views

Determine reference for reference-compressed SRA file

Note: this question was also asked on Github. I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an ...
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2 votes
1 answer
95 views

What is the recognized way to reference accession data (.sra files) from NCBI as a URI?

I would like to assign a URL/URI to accession runs (i.e. SRR IDs) from the NCBI short read archive. In program listings, I used to list them as ftp:// URLs, ...
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  • 309
5 votes
6 answers
2k views

How to extract metadata from NCBI's short read archive (SRA) for a few runs?

I wish to extract metadata from a list of runs on NCBI's short read archive. For instance, I'd like to extract the library name ("HS0798") from the following run info: https://trace.ncbi.nlm.nih.gov/...
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  • 309
1 vote
1 answer
99 views

Are there free cloud computing platforms for biology projects? [duplicate]

I want to implement the analysis found in the paper RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics The project id is 281708. ...
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3 votes
2 answers
687 views

Downloading multiple SRA files from several SRA accession IDs does not work

I am trying to download multiple SRA files located in several SRA accessions. Some of my accession numbers are as follows: ...
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6 votes
4 answers
1k views

Convert SRA to FastA

I'm trying to get the FastA files for some accessions (like NC_001416.1). I did not managed to find an FTP server or direct link to these files (I want to get it from command line with ...
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  • 221
5 votes
2 answers
612 views

A reliable fetcher of short read using SRA/ENA accession

I am trying to build a workflow that gets data automatically from databases of sequencing reads (SRA - sequence read archive, ENA - european nucleotide archive). Till now I was pulling everything from ...
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  • 5,327
5 votes
2 answers
2k views

How to get Nanopore MinION fast5 from SRA

I found some Nanopore MinION data on SRA, which I would like to investigate. I use sratoolkit for Illumina data all the time, but I am not sure how to get the ...
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  • 3,551