Tag: fasterq-dump

R and sra toolkit – odd system() behavior ( R, System )

Problem : ( Scroll to solution ) In order to extract some fastq data from NCBI’s sequence read archive I’ve downloaded and installed the sra toolkit for Windows. In order to test if it is setup correctly, I opened cmd, navigated to the directory and typed in the command fasterq-dump…

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sra toolkit

sra toolkit 1 hello I cannot download sra files. I tried prefetch SRR17055838 and gives this error 2021-12-26T13:48:20 prefetch.2.11.2 err: error unexpected while resolving query within virtual file system module – failed to resolve accession ‘SRR17055838’ – The object is not available from your location. ( 406 ) 2021-12-26T13:48:20 prefetch.2.11.2:…

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How to fasterq-dump 10x genomics snATACseq fastq from SRA

How to fasterq-dump 10x genomics snATACseq fastq from SRA 2 I am trying to retrieve fastq files from a 10x genomics snATACseq dataset on SRA. Each run should have 4 fastq files associated with it: I1: Dual index i7 read (optional) R1: Read 1 R2: Dual index i5 read R3:…

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Problems with downloading fastq files from sra-toolkit

Problems with downloading fastq files from sra-toolkit 1 I have been trying to download the fastq files of a single cell RNA experiment from SRX8632237 with the following SRA runs : SRR12108143 SRR12108144 SRR12108145 SRR12108146 The runs show that it has 3 reads per spot (link). However, I am unable…

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