Tag: sra-toolkit

blastn_vdb Error: Cannot open VDB:

blastn_vdb Error: Cannot open VDB: 0 I’m working locally with sra-toolkit. I have downloaded a sra files, validate it with vdb-validate and when I try to do a search with blastn-dbd the following error occurs Error: Cannot get VDB column: ./SRR7443983.sra.SEQUENCE.ACC_PREFIX Anyone knows how to fix it? Thanks blastn_vdb •…

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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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getting paired end datasets from SRA

getting paired end datasets from SRA 0 I am searching SRA by keywords like “paired-end”, but the sra-toolkit seems to only download one file (single-end) about 90% of the time. I just want to make sure my commands are all correct: prefetch SRR13310323 fastq-dump -I –split-files –outdir fastq –gzip –skip-technical…

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