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10 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: ...
vkkodali's user avatar
  • 1,266
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 ...
terdon's user avatar
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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 ...
Poshi's user avatar
  • 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: ...
terdon's user avatar
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3 votes
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How to subset an SRA file for a single chromosome?

After dumping out the reads using fasterq-dump, you'll need to align them first and then extract those that map to your region of interest. I think minimap2 is an ...
Steve's user avatar
  • 3,109
3 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 ...
vkkodali's user avatar
  • 1,266
3 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 ...
StupidWolf's user avatar
  • 1,688
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 ...
Devon Ryan's user avatar
  • 19.6k
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 ...
gringer's user avatar
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3 votes

SRA toolkit and SRA- prefix

@Max_IT and @user3479780 Thanks for bringing this issue to our attention. It has been fixed in EDirect 19.5, which is now available on our public ftp site (See installation instructions here). Please ...
vkkodali's user avatar
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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 ...
aechchiki's user avatar
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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 ...
init_js's user avatar
  • 319
2 votes

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

As reads have equal length, so all 152-bp reads can be split into 76-bp read pairs accordingly. We can get Read1 by trimming the tail 76 bp, and get Read2 by trimming the heading 76 bp. No need to re-...
Zhuqiang Zhang's user avatar
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 ...
James Hawley's user avatar
  • 1,384
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 ...
Fabio Marroni's user avatar
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: ...
Chris_Rands's user avatar
  • 3,948
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 ...
M__'s user avatar
  • 12.6k
2 votes
Accepted

SRA toolkit and SRA- prefix

Using Entrez Direct E-utils, run the following command for your two examples: ...
user3479780's user avatar
2 votes

Shell script to validate fastq issue

Use the SRR accessions, not the sample-IDs you are using. With entrez e-utils, I found the SRR of GSM2683458: ...
user3479780's user avatar
1 vote

sra toolkit fastq-dump comand not terminating

That's an 11GB file and fastq-dump is not a speedster. Without more info the likely answer is that it keeps downloading which might take several hours on poor connection. You can get fastq download ...
ATpoint's user avatar
  • 1,430
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 ...
Carambakaracho's user avatar
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: ...
terdon's user avatar
  • 10.2k
1 vote
Accepted

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 ...
vkkodali's user avatar
  • 1,266
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: ...
terdon's user avatar
  • 10.2k
1 vote

SRA Toolkit execution problem

You can't run Linux binaries on OSX (or vice versa). Download Mac OSX binaries.
Devon Ryan's user avatar
  • 19.6k
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.
Dan Bolser's user avatar
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 ...
Saket Choudhary's user avatar
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. ...
init_js's user avatar
  • 319
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.
M__'s user avatar
  • 12.6k

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