Tag: fasterq-dump

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