Tag: sra-toolkit

Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data? 0 I am trying to download some public RNA-seq data (paired-end) and I have encountered that there are some samples that have the same GEO Accession but different SRR number (and different sizes). Therefore, when I download…

fastq-dump – connection failed 1 Hi, I need to install a specific RNA sequence data using sra toolkit. I installed the toolkit using this command: sudo apt install sra-toolkit Then confirmed installation by which fastq-dump and got this /usr/bin/fastq-dump But when downloaded SRR21627290 fastq-dump –stdout -X 2 SRR21627290 I got…

Error: connection failed and certificated verification failed in fastq-dump 0 I am currently using Ubuntu-18.04 on wsl2. I saved ext4.vhdx on my D: drive and linked the path to it (to solve the problem of data capacity). After that, I tried to use sra-toolkit for ‘fastq-dump –stdout -X 2 SRR390728’,…

fastq file 1 Hi everyone, I have a question. Apart from using the “fastq-dump –split-files” command to download files, is there another command that can split the forward and reverse files if I download my fastq file as one single file? actually, i have problem with sra-toolkit and i should…

fastq-dump unable to separate fastq files from scRNA-seq SRA files 1 Hi all, I recently downloaded a scRNA-seq file (SRR12661516) using sratoolkit. Then I needed to get the fastq files as I plan to upload the resulting fastq files to 10X genomics cloud for a new analysis. I used fastq-dump…

zero byte files in sratoolkit.3.0.1-ubuntu64 0 I have downloaded sratoolkit for ubuntu. After getting the tar file and unzip it, I added the bin path to the Path variables as well. When I run which fastq-dump, it correctly identifies the path. However, when I run vdb-config -i or vdb-config –interactive…

sra-toolkit not working 2 I downloaded sra-toolkit from sra website for 64bit Windows. After extracting I tested it from bin folder: sra-toolkit\bin> fastq-dump –stdout -X 2 SRR390728 but it throws error: 2015-12-15T09:54:40 fastq-dump.2.5.5 err: item not found while constructing within virtual database module – the path ‘SRR390728’ cannot be opened…

Name Last modified Size Parent Directory – sra-sdk_2.3.5-2+dfsg-1.debian.tar.xz 2014-07-30 15:22 8.8K sra-sdk_2.3.5-2+dfsg-1.dsc 2014-07-30 15:22 2.1K sra-sdk_2.3.5-2+dfsg.orig.tar.xz 2014-07-30 15:22 2.1M sra-sdk_2.8.1-2+dfsg-2.debian.tar.xz 2017-04-02 00:22 13K sra-sdk_2.8.1-2+dfsg-2.dsc 2017-04-02 00:22 2.1K sra-sdk_2.8.1-2+dfsg.orig.tar.xz 2017-01-24 10:35 2.8M sra-sdk_2.9.3+dfsg-1.debian.tar.xz 2018-10-23 23:07 3.7M sra-sdk_2.9.3+dfsg-1.dsc 2018-10-23 23:07 2.1K sra-sdk_2.9.3+dfsg.orig.tar.xz 2018-10-23 23:07 3.7M sra-sdk_2.10.9+dfsg-2.debian.tar.xz 2021-02-05 03:50 3.7M sra-sdk_2.10.9+dfsg-2.dsc 2021-02-05 03:50…

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 •…

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…

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…