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How to download RNA files in the easiest way? (from NCBI's SRA)

I want to download a list of around 2000 RNA-sequence files. My approach of doing it is very inefficient:

  1. I go to https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=search_obj
  2. Type in the name of experiment. Fx. SRR1186053.
  3. Then I click my self into: https://trace.ncbi.nlm.nih.gov/Traces/sra/view=search_seq_name&exp=SRX483399&run=&m=search&s=seq, where I click download on the FASTA file (because I don't know whether to need FASTQ instead...)
  4. After the file is downloaded, I filter it from the metadata (time, length, etc.) and concatenate all the smaller sequence to one big sequence. This is done in a simple C++ program I have built.
  5. At last, I get all k-mers from this sequence, and add them to a data structure I have built.

I would love to know if there is an easier way to do this. How do I make one bulk download?

Example of a list:

  • blood SRR1186053 8399571400 5850
  • blood SRR1186053 8399571400 5850
  • blood SRR805782 724114625 412
  • blood SRR837459 1313374050 841 ...
rna-seq rna-seq next-gen sequencing genome
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written by GoldenRetriever • GoldenRetriever

3 answers

You can use the sratools:

https://github.com/ncbi/sra-tools

specifically fastq-dump

https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump

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written by Carambakaracho Carambakaracho

I couldn't delete this question after I added it. But I quickly found out that NCBI SRA have a nice toolkit for fetching files using the command line. Specifically, I use prefetch <name of gene> but use xargs to fetch many files: cat <filename> | xargs -i prefetch {}, where filename is a file containing all the genes that I want. I.e. I feed the genes into the square brackets.

But thanks for the answers anyway. Much appreciated.

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written by GoldenRetriever • GoldenRetriever

Use sra-explorer. Details on how to use here: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

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written by GenoMax GenoMax

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