Tag: SRA

can i skip cutadapt?? – User Support

recently i receive rowdata from NGS center..and i start analysis using QIIME2 i want ‘cutadapt’, so i ask primer sequence to NGS center..but center reply to me “it is secret” if it is neccessery, i request to NGS center…. thank u for reading Hi @svbreqwaiu01, You do not need to…

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Screen.seqs result varying – Commands in mothur

I have a data set of 2×150 reads of 54 pairs of 16S v4 metagenomic sequences from NCBI sra of gastritis patients. When I previously ran the sequences through mothur, the screen.seqs after silva alignment removed sufficient number of sequences. mothur > screen.seqs(fasta=current, count=current, start=2, end=13426)Using Ulcer_Donors\stability.trim.contigs.count_table as input file…

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How To Download Geo Data? Update New

Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Images related to the topicBioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics…

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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…

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GEO Browser – GEO – NCBI

Filter Mus musculus TSV Brian P. Hermann GSE109033 10x Genonics Drop-seq single-cell RNA-seq of isolated Adult ID4-EGFP mouse spermatogonia, spermatocytes, spermatids & steady-state spermatogenic cells Expression profiling by high throughput sequencing Mus musculus 8 MTX TSV SRA Run Selector Brian P. Hermann Nov 06, 2018 GSE109037 10x Genomics Drop-seq single-cell…

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Phylogenomic analysis of Syngnathidae reveals novel relationships, origins of endemic diversity and variable diversification rates | BMC Biology

Stölting KN, Wilson AB. Male pregnancy in seahorses and pipefish: beyond the mammalian model. Bioessays. 2007;29:884–96. PubMed  Google Scholar  Whittington CM, Friesen CR. The evolution and physiology of male pregnancy in syngnathid fishes. Biol Rev Camb Philos Soc. 2020;95:1252–72. PubMed  Google Scholar  Rosenqvist G, Berglund A. Sexual signals and mating…

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Search SRA Gateway for Metagenomics Data Wiki

Abstract The Sequence Read Archive (SRA)(https://www.ncbi.nlm.nih.gov/sra) houses all publicly available biological DNA sequence data to enhance reproducibility, reduce redundancy, and to allow for new discoveries by comparing data. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms and is growing at the alarming rate of 10…

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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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A mammalian methylation array for profiling methylation levels at conserved sequences

Designing the mammalian methylation array The CMAPS algorithm is designed to select a set of Illumina Infinium array probes such that for a target set of species many probes are expected to work in each species (see “Methods” section). Array probes are sequences of length 50 bp flanking a target CpG…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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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…

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MARS seq alingment

MARS seq alingment 0 Hello everyone, new here and also new to the field. was asked to create a pipeline for RNA seq and after two months of self learning of how to interact with each code im stuck with the program STAR. what im trying to do for now…

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Rockhopper’s alignment issue

Rockhopper’s alignment issue 0 Hi everyone, I’m trying to identify the operons with the Rockhopper tool but at the end of the alignment something strange happens: Aligning sequencing reads from file: SRR6757591_1.sorted.bam Total reads: 10209877 Successfully aligned reads: 9358027 92% (>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome) Aligning…

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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:…

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Import problem: Not a(n) QIIME1DemuxFormat file – Technical Support

Hi @emiliomastriani, Did you download the sequences form sra?This previous question may give you some help: Hi there, I am familiar with QIIME1 but relatively new with QIIME2. I have gotten my raw file in the past from a facility in the CASAVA pair ended demultiplexed format and I had…

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16S rRNA gene amplicon sequence data from sunflower endosphere bacterial community

doi.org/10.1016/j.dib.2021.107636Get rights and content Abstract Insights into plant endosphere bacterial diversity and exploration of their bioincentives in the formulation of biofertilizers promise to avert ecological disturbances. Here, we presented the sequence dataset of the endophytic bacterial community from the roots and stems of sunflower obtained from farmlands in Itsoseng and…

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Complete mitochondrial genome sequencing of Oxycarenus laetus (Hemiptera: Lygaeidae) from two geographically distinct regions of India

Genome organization and structure of O. laetus The MiSeq data of BTI and CBE samples of O. laetus was submitted to the NCBI SRA database under the accession numbers SRR11024516 and SRR11024517, respectively. The study was done to understand whether there exists a different species of the genus Oxycarenus similar…

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Correction of sequencing error using only Bowtie?

Correction of sequencing error using only Bowtie? 1 Dear All, I was reading an old paper published on Nucleic Acid Research about the sequencing of a bacterial genome. The authors performed a primary assembly using 454 reads (36 coverage), and the resulting contigs were scaffolded using a jumping library with…

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NCBI’s Efetch not working

Any help would be much appreciated. My goal is to run the following for loop to generate a list of sample_id (which is actually isolation site) for a list of SRAs. However I get an error (see below) for each and every SRA. for sra in `awk ‘NR>1{print $1}’ metadata.txt`…

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Unable to download fastq files in parallel / SOS

Unable to download fastq files in parallel / SOS 0 Hi! Very new to all this so bear with me if I’m using incorrect terminology. Also english is my second language. I’m trying to download my fastq files in parallel but it doesn’t work and I keep receiving this error:…

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get read length from sra

get read length from sra 0 hi everyone ! i need a method “api” to retrive reads length form sra thanks in advance rna api seq • 44 views • link updated 38 minutes ago by Renesh &starf; 2.0k • written 2 hours ago by Sar • 0 Login before…

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Answer: Error during prefetch

Maybe a connection problem, not unusual with NCBI. There is no need to bother with the NCBI Toolkits, you can get fastq files directly with links from e.g. sra-explorer.info If you visit that website (which is a wrapper around the NCBI and ENI APIs) and enter your accession it will…

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Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data. 0 Hi all, asking for a colleague, I’m looking for human non-poly-A mRNA that would end with a specific pattern ( say CCGCAT ). is it possible to find this in a RNA-SEQ data ? (e.g: www.ncbi.nlm.nih.gov//sra?term=SRR059132…

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Bioinformatics Scientist | Washington, DC

Bioinformatics Scientist | Washington, DC | Kelly Services Location: Start New Search: bioinformatics scientistfluidicsbiodefensemicrobiomedna sequencingngsrnabioinformaticsnihsurgeglobal healthvaccineinfectious diseasecomputationalallergymicrobiologymachine learningclinical researchbethesdahiv aids Kelly ServicesWashington, DC Full-time Perform a wide variety of complex procedures and techniques in support of RTB including Affymetrix fluidics and hybridization protocols; high-throughput TaqMan processing; microarray data analysis; high-throughput…

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Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Significance The collection of large amounts of whole-genome sequencing data allowed for identification of mutational signatures, which are characteristic combinations of substitutions in the context of neighboring bases. The clinical significance of these mutational signatures is still largely unknown. In neuroblastoma, we showed that high levels of cytosine > adenine…

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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:…

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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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samtools server vs cluster error

Using inspiration from this thread HISAT2 output direct to bam, I’m attempting to run this command. The shell variables in this case represent paths to files/locations that make sense and in fact this command runs fine on my Ubuntu 18.04 LTS server using hisat 2.1 and samtools 1.10 (this seems…

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Postdoctoral researcher Microbiome Bioinformatics 100%, Zurich, fixed-term

Postdoctoral researcher Microbiome Bioinformatics 100%, Zurich, fixed-term 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global microbial biodiversity as part of the Microbiota Vault initiative’s efforts to preserve our microbial…

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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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Postdoctoral researcher: Microbiome Bioinformatics

In der aktuellen Covid-19 Situation laufen die Rekrutierungen weiter. Es kann dabei allerdings zu Verzögerungen kommen. Vielen Dank für Ihr Verständnis. 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global…

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SRA/ENA library layout is inconsistent with the data source

project number: PRJNA505380 An example of Run accession: SRR8244780 Issue: Inconsistency between the library layout of Run and data source. As the library layout both in ENA and SRA labeled, Runs in Bioproject PRJNA505380 should be pair-end reads data. But some of them only have a single fastq and without…

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Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 I was not expecting this — not sure what to make of it…

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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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Where do I get a WES dataset of size

Where do I get a WES dataset of size <1GB 1 Can someone please tell me from where can I get the WES or WGS dataset of size <1GB WGS WES genomics • 164 views Just browse sra-explorer.info for datasets. I doubt you can meaningfully query for file size as…

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SRA splitting for each metagenome-assembled genome

Job:SRA splitting for each metagenome-assembled genome 0 Hi everybody, we obtained viruses from water and sequenced them with Illumina. we formed different metagenomic-assembled genomes and get a Bioproject number and Biosample numbers (for each of them). Now, i should do SRA submission. But i cannot submit for my all genomes…

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Python fast way to get ONLY MAIN metadata for GSE ? (not walking through thousands underlying GSM-samples : slow or even endless)

  Not Python but using EntrezDirect you can get: $ esearch -db bioproject -query “GSE118723” | esummary | xtract -pattern DocumentSummary -element Project_Description Quantification of gene expression levels at the single cell level has revealed that gene expression can vary substantially even across a population of homogeneous cells. However, it…

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MinION Data Examples (FAST5) Database

MinION Data Examples (FAST5) Database 0 Hello everyone, I am constructing a pipeline to analyze Oxford Nanopore MinION data. I have start from FAST5 files and for some optimizations I will try multiple tools for each step. So I will need several datasets to try. As I see most of…

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GEO submission when I have raw data in SRA

GEO submission when I have raw data in SRA 0 I am trying to submit my scRNA-seq data to GEO. GEO submission guidelines state that I should upload metadata, raw and processed data. And they submit the raw data to SRA on my behalf. But I already submitted my raw…

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command not found, what is wrong?

fastq-dump: command not found, what is wrong? 0 I have downloaded a tar of SRA toolkit, unzipped and installed it. I have also done the binary installation where you specify the path and I think I’ve done it correctly. Now, I try to use fastq-dump and it runs when I…

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