9 votes

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

Entrez Direct is perfect for this sort of thing. You can do something like this: ...
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  • 1,116
6 votes
Accepted

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

First of all, the brace expansion you tried to use isn't valid. While bash can expand {1..3} to 1 2 3, it has no way of knowing ...
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  • 7,957
5 votes
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Convert SRA to FastA

Finally, I found an alternative to the SRA translation: a link that works! For those of you interested in knowing how to download FastA files from NCBI using an accession number, try the following ...
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  • 221
5 votes
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Using variables with fasterq-dump?

You have an obvious error in your shell script that should have given you an error message: sra_code = "DRR163""$i" Should be: ...
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  • 7,957
3 votes

How to extract metadata from NCBI's experiment?

You'll want something like: esearch -db sra -query SRX1596422 | efetch -format runinfo This will produce a CSV output to the screen with columns containing the ...
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  • 19.3k
3 votes

How to get Nanopore MinION fast5 from SRA

When I was trying to upload MinION data to SRA, they wouldn't allow me to upload only the raw signal data (i.e. FAST5 files). Every file needed to contain a FASTQ sequence, and this sequence was ...
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  • 11.5k
2 votes

How to get Nanopore MinION fast5 from SRA

I would suggest trying an alternative way, as the FAST5 is a fairly new entry in SRA - 6 public datasets as of today. You can search the ERX/ERR entry you got from SRA in ENA and either (1) direct ...
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  • 2,614
2 votes

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

Here's a very crude script version, which should work without downloading fancy software tools. It will only work as long as the website stays in its current layout. It extracts the particular ...
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  • 309
2 votes
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Fasterq-dump: --split-spot or -concatenate-reads?

Fasterq comes from the latest version of sratools. So if you check the manual , it says the equivalence is: fastq-dump SRRXXXXXX --split-3 --skip-technical fasterq-dump SRRXXXXXX In older versions ...
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  • 1,638
2 votes
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How to split FASTQ reads without re-running `fastq-dump`?

My comment above mentions the slow IO for the Python code (it was iterating at ~ 3600 reads/s, which, for a FASTQ with 500M reads would take ~1.6 d to complete), so I tried an alternative method that ...
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  • 1,077
2 votes

What happened to sra ftp server?

NCBI appeared at least in part to shift onto Google Cloud buckets, one previous OP raised a question about access via GCP (I think the question was closed). Fundamentally, traditional FTP is not ...
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  • 6,967
2 votes

What happened to sra ftp server?

SRA moved all of the data to the cloud per https://ncbiinsights.ncbi.nlm.nih.gov/2020/02/24/sra-cloud/ You can still download data for free using sratoolkit as ...
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  • 1,116
2 votes

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

After checking with file.exists(), I would suggest you try the same command with another SRA run. It may happen that some runs are not accessible for reasons I do ...
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2 votes

Convert SRA to FastA

Here is a Biopython solution via Entrez utilies, simply copy the code into a python script and execute it: ...
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  • 3,462
1 vote

Convert SRA to FastA

You can either do this directly as you show in your answer or, for a more sophisticated and flexible approach, use NCBI's edirect tool: ...
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  • 7,957
1 vote
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Why am I getting empty expression data from GEO?

I am sure the data is legit, you are just approaching it incorrectly. getGEO is an application for microarray data, not for digital count data such as (sc)RNA-seq, therefore what you aim to do is ...
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  • 2,706
1 vote

Genome QC + Assembly Pipeline semantics

Maybe take a look at workflow management systems, like snakemake Nextflow Toil Cromwell Admitted, each of those adds their additional learning curve. However, especially snakemake is not so much ...
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1 vote
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SRA Toolkit and lebanese data

Your command is fine. It is working as expected. Did you intend to include -X 5 in your command? That restricts the number of spots to 5. If you drop it, you will ...
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  • 1,116
1 vote

Fastq-dump script download X spots or all

You don't need to copy your arguments into variables, you can just use $1 directly. Anyway, this should be enough: ...
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  • 7,957
1 vote

SRA Toolkit execution problem

You can't run Linux binaries on OSX (or vice versa). Download Mac OSX binaries.
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  • 19.3k
1 vote

Determine reference for reference-compressed SRA file

Run align-info to see the references used. Run prefetch </path/to/sra/file> to download missed references.
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1 vote

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

The nomenclature is no longer being followed as NCBI is moving all the files to S3/Google cloud. pysradb allows you to fetch the metadata and get the URLs for each individual SRR. See examples in this ...
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1 vote

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

I've been told by the support team that there's a way to pull it out in csv form by GETting the following URL, replacing <SRRNUMBER>, with, e.g. ...
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  • 309
1 vote

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

Its got to be the SRA Toolkit The way I would do it (a traditional Perl digger) doesn't work on the Tracer NCBI site, at least not readily and dumping the XML is likewise unlikely to succeed.
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  • 6,967
1 vote
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Are there free cloud computing platforms for biology projects?

If you're getting started with a project and need some free computational resources you should look at https://galaxyproject.org/. There are some free servers that you may be able to use. However, ...
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  • 3,041
1 vote

A reliable fetcher of short read using SRA/ENA accession

Here are two python functions I use for getting stuff from ENA based on an accession: ...
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  • 3,201
1 vote
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A reliable fetcher of short read using SRA/ENA accession

Apparently there is no 100% reliable solution, but in the most cases, you should be able to use the enaBrowserTools python scripts (enaDataGet) to quite reliably download data. The run ERR2135453 is ...
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  • 5,287

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