Hello i downloaded single cell RNA data from AWS such as this example https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR21834806&display=data-access
wget https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21834806/SRR21834806
is there a way to convert what was already downloaded into R1 and R2 using fastq-dump, preferably original format fasta?
1 answer
You can use fasterq-dump: https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump
An accession is not a file, it is a container of files. Depending in the data submitted to NCBI, the container will have just one file or many files. Because of that, best practice is to always specify a directory.
example: $fasterq-dump /home/user/data/SRR000001
incorrect: $fasterq-dump /home/user/data/SRR000001/SRR000001.sra
That will spit out R1 and R2 fastq by default. It's part of sra-tools:
conda install bioconda::sra-tools
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If you can download the original data files using
aws clithe use thes3links on that page you linked:s3://sra-pub-src-13/SRR21834806/6438-RMM-0002_12_S12_L002_I1_001.fastq.gz.1. They will require not conversion/changes.Note: Not sure if this data allows free egress. If it does not then you will need a AWS account and payment.
A really neat tool for those smaller use-cases is sra-explorer.info: type in the accession number, tick the library you want to download, press 'Add X to collection', click 'X saved datasets' button, then you get many various commands you can copy paste to wget/curl/ascp all fastq or sra files from various sources.
Well aware of the tool. But this is a 10x dataset and those are sometimes iffy to download from SRA. Links I referred to are the original files uploaded so they may sometimes be the best bet to get the correct data.