Tag: SRR

3 Simple Ways to Download FASTQ files | by Vijini Mallawaarachchi | The Computational Biology Magazine | Dec, 2023

A detailed overview of 3 ways to download FASTQ files of SRA runs from NCBI As bioinformaticians, the National Center for Biotechnology Information (NCBI) is one of the most important resources we use to get data. NCBI plays a crucial role in our research community due to its extensive databases…

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Bowtie mapping for single_end read

Bowtie mapping for single_end read 1 bowtie –threads 5 -X 1000 -m 1 -v 2 –best –strata –sam IndexedGenome ${DATA_DIR}${SRR_ID}.trim.fastq > ${SAM_DIR}${SRR_ID}.sam Hi All, I am using the above script to map single_end ChIP-Seq reads. The percentage of the aligned reads is around 20%. How can I modify the script…

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issue in RNA -seq analysis

Forum:issue in RNA -seq analysis 0 hello all. i am working on RNA seq analysis. i would like to know following things: first i downloaded genome fasta file for non-coding rna from ensembl and got the gtf file for hg38 from there itself. performed hist2 and got 17% alignment for…

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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,…

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Valneva Reports Positive Pivotal Phase 3 Immunogenicity Data in Adolescents for its Single-Shot Chikungunya Vaccine Candidate

Saint-Herblain (France), November 13, 2023 – Valneva SE (Nasdaq: VALN; Euronext Paris: VLA), a specialty vaccine company, today reported positive pivotal Phase 3 immunogenicity data in adolescents for its single-dose chikungunya virus (CHIKV) vaccine candidate VLA1553. These results complement the initial Phase 3 safety data the Company reported for the…

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Valneva Reports Positive Pivotal Phase 3 Immunogenicity

Saint-Herblain (France), November 13, 2023 – Valneva SE (Nasdaq: VALN; Euronext Paris: VLA), a specialty vaccine company, today reported positive pivotal Phase 3 immunogenicity data in adolescents for its single-dose chikungunya virus (CHIKV) vaccine candidate VLA1553. These results complement the initial Phase 3 safety data the Company reported for the…

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trying to use the API for edirect tool (NCBI)

trying to use the API for edirect tool (NCBI) 1 Hi, I’m new to bioinformatics, so I apologize if my question seems a little bit basic. I wanted to use the tool Edirect to retrieve information about a list of samples that I have generated. I work on a cluster,…

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Solved Download fastac.ac.sh, fastac.loop.sh and

Transcribed image text: Download fastac.ac.sh, fastac.loop.sh and runinfo.csv, Answer the questions below: 1. Run the bash script fas tqc. qc. sh. How many NEW files are generated under directory reports/ after your script runs successfully? 2. Edit the file fastqc. loop. sh so the script successfully loops through the SRR…

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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….

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Multiple RNA-seq fastq files for one sample in GEO database

Multiple RNA-seq fastq files for one sample in GEO database 0 Hello, I’m trying to analyze public RNA-seq data obtained from GEO database. But I have a trouble now about how to handle some data. The representative dataset is GSE88945 (PRJNA349164). The number of samples is just three but the…

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SRA obtained metagenomic reads appears to corrupt

Hello, I am trying to run SingleM on data obtained using sratoolkit (2.10.7) I used prefetch SRR2103020 to download and fastq-dump –outdir ./fastq –split-e ./SRR2103020/SRR2103020.sra to split. when I check the file : head SRR2103020_1.fastq @SRR2103020.1 D7RS0RN1:177:C12Y0ACXX:3:1101:1404:2079 length=93 AATGTGGACAGCGCCGTCTTCAAACAGGCGCTGTCCAGCTAGCAGCTCAACGCTCCGCGCCGCCGTCTTCGCCGTCTTCAGGCAGGGGGAGAA +SRR2103020.1 D7RS0RN1:177:C12Y0ACXX:3:1101:1404:2079 length=93 @BCFFFDDHHHHHJJJGIJIBHHIJJCH?HBG<GIG@HEGIGFIFG@>CGHHHFFFDD@BB::BD@B??CDBDD@BD@DA@CCDDBD###### @SRR2103020.2 D7RS0RN1:177:C12Y0ACXX:3:1101:1440:2113 length=93 GGTATAAGTTCTATGTGTAATGAACCACAGAGTTATCAAAAAACTCAAGATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG +SRR2103020.2 D7RS0RN1:177:C12Y0ACXX:3:1101:1440:2113 length=93…

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SRA toolkit access denied

SRA toolkit access denied 1 I was trying to get data from NCBI using SRA toolkit. As usual, I did prefetch and faster-dump commands, but access denied error was occurred. prefetch.2.11.0 err: query unauthorized while resolving query within virtual file system module – failed to resolve accession ‘SRR——‘ – Access…

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fasta – adding multiple files in folder and zipping in loop

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

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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…

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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…

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Obtaining TPM values from STAR alignment and counts with featurecounts using R’s tidyverse syntax (dplyr and tidyr)

Hello! I have a table of counts that I got by aligning rna seq samples with STAR and using featureCounts, and my goal is to get TPM values for each gene of the table. As a first step, I imported my table into R and modified it a bit to…

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Missing columns in meta table from SRA Selector

Unfortunately there is not enforced standard of what metadata must make into the SRA, it is very frustrating actually and makes reproducing any analysis needlessly complicated. You can look at what EBI fields are there, and sometimes they produce more fields than SRA: pip install bio then look at the…

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Sub-millisecond conformational dynamics of the A2A adenosine receptor revealed by single-molecule FRET

Protein expression, purification and labeling The gene encoding the human A2AAR (UniProt C9JQD8) C-terminally truncated after residue Ala 316 (Supplementary Fig. 1a) was synthesized de novo (Eurofins). The nucleotide sequence was optimized for Leishmania tarentolae expression with the GeneOptimizer software (ThermoFisher Scientific). KpnI restriction site was introduced at the C-terminus and…

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Problem with fatsq-dump

Problem with fatsq-dump 0 Hi, I am absolutely new in NGS data analysis and have just started working in centos. I installed sratoolkit with the commands : conda create –n sratoolkit_env –y conda activate sratoolkit_env conda install –c bioconda sra-tools –y Then as given in the Biostar Handbook (Bioinformatics Data…

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RNA-SEQ

RNA-SEQ 1 Hi everyone, I am having issues with my RNA-seq data. Specifically, I have data for a single sample that includes two different SRA numbers. Although my data is paired-end, I am uncertain whether each SRR number corresponds to the forward or reverse reads, or if they represent technical…

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1 is not found in chromosome sizes file

1 is not found in chromosome sizes file 0 I am trying to convert bedGraph to bigWig file with bedGraphToBigWig. but I always get “1 is not found in chromosome sizes file”. I used the following script macs2 callpeak -c SRRc_sorted.bam -t SRRe_sorted.bam -B –nomodel –extsize 200 –SPMR -q 0.01…

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Why 0/0 genotype refers to SNP and ALT != REF (in vcf file after freebayes)

Why 0/0 genotype refers to SNP and ALT != REF (in vcf file after freebayes) 1 Good morning, Could you please explain me, why 0/0 genotypes in vcf are SNPs? According to this description of GT: 0/0 the sample is a homozygous reference 0/1 the sample is heterozygous (carries both…

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KEGG T01001: 63826

Entry 63826             CDS       T01001                                  Symbol SRR, ILV1, ISO1 Name (RefSeq) serine racemase   KO K12235   serine racemase [EC:5.1.1.18] Organism hsa  Homo sapiens (human) Pathway hsa00260   Glycine, serine and threonine metabolism hsa00470   D-Amino acid metabolism hsa01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:hsa00001] 09100 Metabolism  09105 Amino acid metabolism   00260 Glycine, serine and threonine metabolism    63826 (SRR)  09106 Metabolism of…

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djghjc

djghjc 1 hi, does anyone know how to find the sample_id for srr? bioinf • 130 views Using EntrezDirect: $ esearch -db sra -query SRX19366692 | elink -target biosample | esummary | xtract -pattern DocumentSummary -element Identifiers BioSample: SAMN33293805; SRA: SRS16763294; EDLB-CDC: PNUSAE127503 Login before adding your answer. Read more…

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expanding sequence

expanding sequence 0 i have some SSR region sequence in the form of AG(3), CTC(23), GGGTCA(21). I HAVE TO MADE ONE SINGLE SRR SEQUENCE LIKE AGAGAGCTCTCTCTCTCTC……. so on. can anyone suggest how i can do it in excel or using any code. manually it is very difficult to decode it….

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bedtools intersect error: Invalid record in file

Hello to all I am trying to run bedtools intersect with vcf file and a bed file (my goal is to add the depth data to my VCF) I get an error running this command: bedtools intersect -a depth.bed -b fish.vcf -wa -wb > $out The error: “Error: Invalid record…

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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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Re-analysis of multiple scRNAseq data as a combined new one

Re-analysis of multiple scRNAseq data as a combined new one 0 Hi all, There are so many regions in brain.The cortex itself is of many types.I found many single cell RNA seq studies which focus on different regions eg- gse … somatosensory cortex dropseq year 2015 gse….. primary visual cortex…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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FreeBayes VCF output with FORMAT unknown

Hey, I am looking for a way to add samples ID names to the FORMAT in my vcf file. I have 10 sorted Bam files. I used Freebayes to create vcf files and my next step is merging all 10 files for VcfSampleCompare. And for that I need to define…

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bcftools consensus still returns “Could not parse the header” error

bcftools consensus still returns “Could not parse the header” error 0 I attempted to create a consensus fasta file using bcftools, i.e. bgzip -c All_SRR_SNP_Clean.vcf > All_SRR_SNP_Clean.vcf.gz tabix All_SRR_SNP_Clean.vcf.gz cat $ref| bcftools consensus $vcf_dir/All_SRR_SNP_Clean.vcf.gz > consensus.fasta where $ref is the path to a Drosophila reference genome fa and the vcf…

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