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….

Continue Reading Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri

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,…

Continue Reading Efficient Bulk Data Retrieval from NCBI BioProject

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…

Continue Reading Best command line tool for downloading sequencing reads

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….

Continue Reading SRR download using fasterq-dump

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…

Continue Reading Bulk RNAseq Standard Data Processing Pipelines

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…

Continue Reading Downloading the fastq files did not well going; read in the fastq files are all the same

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…

Continue Reading issue regarding download SRA file in bulk

fasta – adding multiple files in folder and zipping in loop

fasta – adding multiple files in folder and zipping in loop – Bioinformatics Stack Exchange …

Continue Reading fasta – adding multiple files in folder and zipping in loop

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…

Continue Reading Public single cell rna-seq with only one fastq file. How can I handle it?

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…

Continue Reading Prefecth-orig and fasterq-dump not working when downloading SRA files (v3.0.5)

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…

Continue Reading fasterq-dump outputs “Cannot use ‘–ngc’ as ngc file.”

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…

Continue Reading SRA download

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…

Continue Reading Question about a public scRNA dataset(single end)?

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)…

Continue Reading How do I get separate ADT / CITE-seq fastq’s from single SRA / BAM files? (originally generated from cellranger)

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…

Continue Reading parallel downloads from SRA with SRA toolkit or other ways to speed up downloads

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…

Continue Reading R and sra toolkit – odd system() behavior ( R, System )

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:…

Continue Reading sra toolkit

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:…

Continue Reading How to fasterq-dump 10x genomics snATACseq fastq from SRA

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…

Continue Reading Problems with downloading fastq files from sra-toolkit