Questions tagged [sratoolkit]
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30 questions
6
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4
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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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6
votes
1
answer
78
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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 ...
- 5,110
5
votes
6
answers
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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/...
- 319
5
votes
2
answers
2k
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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 ...
- 3,601
5
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2
answers
742
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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 ...
- 5,652
4
votes
1
answer
228
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Shell script to validate fastq issue
I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one ...
- 1,854
3
votes
2
answers
881
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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:
...
- 119
3
votes
2
answers
114
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SRA toolkit and SRA- prefix
I am trying to download raw sequence data from the SRA database using the SRA toolkit (v.3.0.2). Unfortunately, the authors of the article I am reading gave SRA numbers (i.e. with the SRA prefix, not ...
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3
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2
answers
742
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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 ...
- 5,652
3
votes
1
answer
277
views
Multiple SRR ID downloaded for single GSM IDs input issue
So here I'm trying to donwload multiple fastq files based on the GSM ID input the script works fine when then input is only SRR id but it runs into error when it is given GSM ID
My small GSM ID input ...
- 207
2
votes
1
answer
2k
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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 ...
- 1,027
2
votes
1
answer
133
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sra toolkit fastq-dump comand not terminating
I ran the following command trying to download a fasta file from NIH but the command doesn't seem to terminate and I get no output file in my repository:
...
2
votes
1
answer
112
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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, ...
- 319
2
votes
1
answer
500
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 ...
- 23
2
votes
1
answer
177
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/...
- 121
1
vote
2
answers
2k
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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:
...
- 1,394
1
vote
1
answer
65
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How to subset an SRA file for a single chromosome?
I used prefetch to get the Pacbio reads of chicken from the SRA database. I want to align these reads against a reference genome, but not all the reads. I am only interested in a particular region on ...
- 105
1
vote
2
answers
146
views
Combing multiple SRA Runs into a single Sample, BioSample or Library
On GEO/SRA some datasets have multiple Runs per Sample, for example this one (96 SRR numbers for 12 BioSample/GEO_Accession/Library Name/Sample Name), and the authors provide their RNA-Seq counts for ...
- 657
1
vote
1
answer
124
views
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 ...
- 13
1
vote
1
answer
72
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:
...
- 59
1
vote
1
answer
136
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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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1
vote
0
answers
309
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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 ...
- 1,027
0
votes
2
answers
243
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 ...
- 1,027
0
votes
1
answer
54
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
0
votes
1
answer
450
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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]...
0
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1
answer
237
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.
...
0
votes
1
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759
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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 ...
- 103
0
votes
3
answers
80
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 ...
0
votes
1
answer
26
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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:
...
- 359
0
votes
1
answer
593
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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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