Questions tagged [sratoolkit]

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1answer
36 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: ...
0
votes
1answer
19 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: ...
1
vote
1answer
37 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: ...
0
votes
1answer
98 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 +...
2
votes
1answer
406 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 ...
0
votes
0answers
16 views

Is there a way to extract reads assigned to a particular taxonomic node from SRA data?

I've noticed that SRR submissions have an 'Analysis' section, where one can see what organisms are enriched in the sample; there is even a great graphic display that uses Krona to highlight what ...
3
votes
0answers
39 views

Determine reference for reference-compressed SRA file

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 internet connection. I got the "name not found ...
2
votes
1answer
60 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, ...
4
votes
6answers
644 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/...
1
vote
1answer
77 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. ...
3
votes
2answers
469 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: ...
6
votes
4answers
612 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 ...
5
votes
2answers
369 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 ...
4
votes
2answers
915 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 ...