Categories
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…
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….
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…
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…
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…
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…
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…
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…
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…
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…
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’,…
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…
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…
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…
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…
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…
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 •…
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…
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…