Tag: sra-toolkit

SRA toolkit (NCBI) – sra to fasta

SRA toolkit (NCBI) – sra to fasta 1 Dear all, At the moment I’m trying to download sequences from the Sequence Read Archive (SRA) from NCBI and put them into fasta format. For this I downloaded the SRA-toolkit of NCBI and used the following code: set PATH=%PATH%;C:\Users\Admin\Desktop\sratoolkit.2.9.0-win64\sratoolkit.2.9.0-win64\bin prefetch –max-size 100000000…

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SRR download using fasterq-dump

SRR download using fasterq-dump 1 Hello, I have downloaded the sra-toolkit from Anaconda (anaconda.org/bioconda/sra-tools) and downloaded an .sra file using the command: prefetch SRR20073591. The .sra file is located here: /faststorage/project/Biof/testdir/SRR20073591/SRR20073591.sra. When I navigate to the directory and use this command: fasterq-dump SRR20073591.sra, I get an output file called SRR20073591.fastq….

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Bulk RNAseq Standard Data Processing Pipelines

Pipelines and parameters used to process data on the BioBox platform   Pipeline for processing public data to sample gene counts SRA-Toolkit is used to fetch the raw files using fasterq-dump -e 3 The files are passed to Kallisto for quantification using kallisto quant -t 3 If the sample is…

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Debian binary debdiff for sra-sdk

Version in base suite: 3.0.3+dfsg-5 Version in overlay suite: 3.0.3+dfsg-6~deb12u1 Base version: sra-sdk_3.0.3+dfsg-5 Target version: sra-sdk_3.0.3+dfsg-6~deb12u1 Base files: libncbi-ngs-dev_3.0.3+dfsg-5_amd64.deb libncbi-ngs3-dbgsym_3.0.3+dfsg-5_amd64.deb libncbi-ngs3_3.0.3+dfsg-5_amd64.deb libngs-c++-dev_3.0.3+dfsg-5_amd64.deb libngs-c++3-dbgsym_3.0.3+dfsg-5_amd64.deb libngs-c++3_3.0.3+dfsg-5_amd64.deb libngs-java_3.0.3+dfsg-5_amd64.deb libngs-jni_3.0.3+dfsg-5_amd64.deb sra-toolkit-dbgsym_3.0.3+dfsg-5_amd64.deb sra-toolkit_3.0.3+dfsg-5_amd64.deb Target files: libncbi-ngs-dev_3.0.3+dfsg-6~deb12u1_amd64.deb libncbi-ngs3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb libncbi-ngs3_3.0.3+dfsg-6~deb12u1_amd64.deb libngs-c++-dev_3.0.3+dfsg-6~deb12u1_amd64.deb libngs-c++3-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb libngs-c++3_3.0.3+dfsg-6~deb12u1_amd64.deb libngs-java_3.0.3+dfsg-6~deb12u1_amd64.deb libngs-jni_3.0.3+dfsg-6~deb12u1_amd64.deb sra-toolkit-dbgsym_3.0.3+dfsg-6~deb12u1_amd64.deb sra-toolkit_3.0.3+dfsg-6~deb12u1_amd64.deb lrwxrwxrwx root/root /usr/lib/$(DEB_HOST_MULTIARCH)/jni/libncbi-ngs.so -> ../../x86_64-linux-gnu/libncbi-ngs.so.3.0.3 lrwxrwxrwx root/root /usr/lib/x86_64-linux-gnu/jni/libncbi-ngs.so -> ../libncbi-ngs.so.3.0.3…

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Bug#1040953: bookworm-pu: package sra-sdk/3.0.3+dfsg-6~deb12u1

Package: release.debian.org Severity: normal Tags: bookworm User: release.debian….@packages.debian.org Usertags: pu X-Debbugs-Cc: sra-…@packages.debian.org Control: affects -1 + src:sra-sdk [ Reason ] Per #1039621, the new libngs-jni package accidentally wound up with bad content (unexpanded variables in the key symlink’s source *and* target) that rendered it useless. [ Impact ] This package’s…

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issue regarding download SRA file in bulk

issue regarding download SRA file in bulk 0 I want to download a bulk amount of SRA files with sra-toolkit with a bash scripting code but it is not working can it be fixed? #!/bin/sh input=”/home/omic/Downloads/peanut16s/input.txt” while IFS= read -r line do echo “fasterq-dump –split-3 $line -O FASTQ_files/” done content…

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SRA-toolkit installation: “fastq-dump not found”

SRA-toolkit installation: “fastq-dump not found” 1 Hello, I’m trying to install SRA-toolkit om my Mac (Apple M2). When I first install it in the terminal the shell manages to find the binary when I write: which fastq-dump And I get an output similar to the one in the guide: /Users/JoeUser/sratoolkit.3.0.0-mac64/bin/fastq-dump…

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fastq.gz how to split.

fastq.gz how to split. 1 Good morning everyone, I am download the fastq files for study GSE132802 through www.ebi.ac.uk/ena/browser/view/PRJNA549083. This is paired fastq file, but I only got one fastq file. I am considering split it. But I am not sure what is the best way to do it. I…

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Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?

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…

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fastq-dump – connection failed

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…

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connection failed and certificated verification failed in fastq-dump

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’,…

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fastq file

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…

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fastq-dump unable to separate fastq files from scRNA-seq SRA files

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…

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zero byte files in sratoolkit.3.0.1-ubuntu64

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…

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sra-toolkit not working

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…

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Index of /debian/pool/main/s/sra-sdk

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…

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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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