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Tag: fasterq-dump
Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri
Cho, C. et al. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat. Genet. 28, 82–86 (2001). Article CAS PubMed Google Scholar Oliva, R. Protamines and male infertility. Hum. Reprod. Update 12, 417–435 (2006). Article CAS PubMed Google Scholar Balhorn, R. The protamine family of sperm nuclear proteins. Genome Biol….
Efficient Bulk Data Retrieval from NCBI BioProject
Efficient Bulk Data Retrieval from NCBI BioProject 0 Hello, A month ago, I utilized the SRA Toolkit Pipeline to download Fastq files from a BioProject accession. Following the recommended steps, I generated a list of SRR Names, used prefetch, and then employed fasterq-dump (using parallel-fastq-dump) to obtain the data locally,…
Best command line tool for downloading sequencing reads
Best command line tool for downloading sequencing reads 2 Hello there, I am using enaBrowserTools (enaDataGet) for bulk downloading raw reads from ENA in a pipeline of mine. The last few weeks I noticed that I am getting this error message a lot when I use this tool Error with…
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…
Downloading the fastq files did not well going; read in the fastq files are all the same
Downloading the fastq files did not well going; read in the fastq files are all the same 1 Hello everyone, I want to download fastq files of SRR7749705 (2×75bp). I used fasterq-dump and got 2 fastq files, SRR7749705_1.fastq and SRR7749705_2.fastq, as expected. However, all the reads in SRR7749705_1.fastq were the…
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…
fasta – adding multiple files in folder and zipping in loop
fasta – adding multiple files in folder and zipping in loop – Bioinformatics Stack Exchange …
Public single cell rna-seq with only one fastq file. How can I handle it?
Public single cell rna-seq with only one fastq file. How can I handle it? 1 hello. I greatly thank you to all of you in this webstie. I downloaded four of samples from PRJNA606815( www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP249907&o=acc_s%3Aa ), using fasterq-dump. The data are single-cell rna seq with 3′ chemistry 10x genomics but…
Prefecth-orig and fasterq-dump not working when downloading SRA files (v3.0.5)
Hi everyone! I am having some problems when I try to download SRA files. Yesterday I was trying to download a set of SRA files using SRA Toolkit 3.0.2 and it didn’t work. I thought that it was a problem with the version, so I just installed the new one…
fasterq-dump outputs “Cannot use ‘–ngc’ as ngc file.”
fasterq-dump outputs “Cannot use ‘–ngc’ as ngc file.” 0 Hey everyone, I am trying to download some fastqs from SRA. I did this a hundred times using the snakemake wrapper “v1.3.2/bio/sra-tools/fasterq-dump” or the command-line. However, I haven’t done it in few month and just wanted to do it again. This…
SRA download
SRA download 0 I’m trying to download a lot of SRA files which are whole genome of animals. average sizes are tens of gigabytes so it takes almost a day to download one individual even if I use SRAtoolkit prefetch and than fasterq-dump. I know there are other ways like…
Question about a public scRNA dataset(single end)?
Question about a public scRNA dataset(single end)? 1 When I downloaded a public scRNA dataset(SRX8492075) from the article ‘Molecular architecture of the developing mouse brain’, why the layout is ‘single’? Anyway, I downloaded it.Then fasterq-dump, I only got one fastq file. enter link description here Could one fastq file run…
How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)
How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger) 0 Hello all. I am trying to pre-process some single cell RNA and ADT (Totalseq-C) data from an GEO SRA, but having some issues getting separate fastq’s for the “CITE-seq” (ADT)…
parallel downloads from SRA with SRA toolkit or other ways to speed up downloads
parallel downloads from SRA with SRA toolkit or other ways to speed up downloads 0 Is there a way to parallelize downloads from NCBI using SRAToolkit on a HPC cluster? I tried using GNU parallel but I can not actually tell if the downloads are doing anything: cat < /home/ptellier/scratch/phillip/data/escc_data/SRA_accessions.txt…
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…
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:…
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:…
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…