Tag: SRR

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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…

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….

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…

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:…

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…

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…

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…

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…