9
Entrez Direct is perfect for this sort of thing. You can do something like this:
$ esearch -db sra -query 'SRR390728' \
| efetch -format runinfo \
| cut -f1,12 -d,
Run,LibraryName
SRR292241,HS0798
SRR390728,HS0798
The runinfo table format has 47 fields including experiment accession, project accessions, bioproject and biosample identifiers and such. You ...
6
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 how to expand {SRR1002678..SRR1184123}:
$ echo {1..3}
1 2 3
$ echo {SRR1002678..SRR1184123}
{SRR1002678..SRR1184123}
Perhaps you meant SRR{1002678..1184123}? But there's no need for this, you already have the accessions in a file ...
5
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 link:
https://www.ncbi.nlm.nih.gov/search/api/sequence/${accession}/?report=fasta
Using wget to download the accession used as example:
wget -O NC_001416.1....
5
You have an obvious error in your shell script that should have given you an error message:
sra_code = "DRR163""$i"
Should be:
sra_code="DRR163""$i"
You cannot have spaces around the = sign in a variable assignment. The line sra_code = "DRR163""$i" means "run the command sra_code with the ...
3
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 meta information available in SRA:
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,...
3
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 extracted from the file and stored in the archive. Given this, I don't expect it will be possible to retrieve signal or event information from SRA. I also don't ...
2
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 download it via ftp or (2) redirect to Galaxy.
Here's a tutorial that might be interesting for you: basically, you first get the archive from ENA, then find ...
2
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 <td> from the webpage, based on a nearby table link ID. and prints it out.
Note: This is brittle. It will only work for library names that fit in a single-...
2
Here is a Biopython solution via Entrez utilies, simply copy the code into a python script and execute it:
from Bio import Entrez, SeqIO
Entrez.email = 'me@email.com'
def get_fasta_from_ids(ids_list):
handle = Entrez.efetch(db='nucleotide', id=','.join(ids_list), rettype='fasta')
for record in SeqIO.parse(handle, 'fasta'):
yield record
...
2
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 of sratoolkit, if you use fastq-dump without specifying --split-3 for paired-end reads, you get the format mentioned, spotID.1 for forward, spotID.2 for reverse:
...
2
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 would cut down on the IO overhead. It's not super efficient, but I ended up using zcat | awk with a switch-case on the line number to stream the data.
# first ...
2
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 not know. I always have problems in accessing sra formatted files and use a workaround to download fastq.
Here is my not official workaround:
runlist<-sraConvert("SRP045534",sra_con=...
1
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 simply not possible by design. Unless you want to start from the raw reads why not taking the at the file named GSE116237_scRNAseq_expressionMatrix.txt.gz provided ...
1
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 more complicated than a standard bash workflow. Those systems do help a lot organize and orchestrate your workflows
1
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 download the entire set of 2563898 spots.
1
You don't need to copy your arguments into variables, you can just use $1 directly. Anyway, this should be enough:
#!/bin/bash
# usage : bash dump_qc.sh <run id> <number of reads>
if [ -z $1 ]; then
echo "ERROR: at least one argument need to be given!" >&2
exit 1
fi
if [ ! -z $2 ]; then
x="-X '$2'"
fi
fastq-dump --split-3 "$x" "...
1
You can't run Linux binaries on OSX (or vice versa). Download Mac OSX binaries.
1
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 notebook.
You can also download an entire project by doing:
pysradb download -p <SRP>
1
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. SRR000001:
https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&db=sra&rettype=runinfo&term=<SRRNUMBER>
So this would be:
# download the file attachment
wget -nv -O foo.csv "...
1
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:
esearch -db nucleotide -query 'NC_001416.1' | efetch -format fasta > NC_001416.1.fa
1
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.
1
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, Galaxy is designed to have pre-fabricated pipelines and a GUI to avoid having to deal with command-line tools. Therefore any sort of custom analysis will have to ...
1
Here are two python functions I use for getting stuff from ENA based on an accession:
import os
import itertools
from urllib.request import urlopen
def fetch_ENA_files(accession):
"""Get the names of the files matching the ENA accession"""
# Get the paths to the files
url = "http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=%s&...
1
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 a special case because the sample submission (ERS1939590) for it has been cancelled. The solution for these reads is to download the data manually from the ftp ...
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