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16,542 results • Page 2 of 331

Hello, I'm a student new to bioinformatics. First, we have transcriptomics data with three replicates and proteomics data with two replicates. I would

OMICS

updated 18 days ago • 이민경[학생](대학원 융합의과학과)

Hello, I'm a beginner in bioinformatics and I have some question about cmap, precisely, regarding Landmark gene selection. I am grateful for all of

L1000 landmark-gene cmap

updated 19 days ago • kim

The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You...The **Biostar Herald** publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too...The **Biostar Herald** publishes user…

herald

updated 19 days ago • Biostar

Dear all, There are still 4 seats available for the onlineccourse on Genome Annotation, which will run from the 13th to the 16th of May. ---------- Course website: https://www.physalia-courses.org/courses-workshops/genome-annotation/ Recent technological advancements in long-read DNA sequencing, coupled with a significant reduction in costs, have rendered the generation of genome assemblies f…

Genome-Assembly Genome-Annotation

updated 19 days ago • carlopecoraro2

am not a bioinformatician by training but am currently learning and trying to develop this skillset starting with the assembly of a new genome, so I appreciate all the help in advance. I am using the VGP genome assembly pipeline...Hi-C data from pooled, unrelated individuals. I am now trying to use this data for scaffolding, starting with pre-processing the Hi-C data by mapping with BWA-MEM2 a…

GenomeAssembly BWA-MEM2 Hi-C

updated 19 days ago • Winter

Hello, I am new to bioinformatics and I have a microbiology background. I am trying to reproduce this same data from the paper [Whole-genome...Hello, I am new to bioinformatics and I have a microbiology background. I am trying to reproduce this same data from the paper [Whole-genome sequencing

WGS Bacterial-Genomics

updated 19 days ago • Ruqaiya

of floating point numbers. I have followed the typical limma-voom workflow (https://ucdavis-bioinformatics-training.github.io/2018-June-RNA-Seq-Workshop/thursday/DE.html) up to the point where it is time to fit the

limma voom R

updated 22 days ago • pairedttest

Hello, I'm doing my masters on Bioinformatics and, as expected, I've hit a sort of roadblock of which I'm unsure how to proceed (my PI isn't very well versed on...bioinformatics). We are researching different treatments for a DSS-induced colitis model in mice. We usually go about this

RNA-Seq edgeR

updated 22 days ago • Guille

in a post title was tricky, so I apologize if the title is unclear. I'll explain in detail below. To start, I have two bed files, one with non-overlapping regions of varying sizes, and one with SNP positions: $ cat A.bed chr1 65564...bed file, and only print these combinations to a new bed file if the SNP is +/- 250,000 bp from the start of the region in A.bed. So, the third bed file, C.…

SNPs BED eqtl bedtools

updated 22 days ago • J

1. Take the genomic VCF file (pf7K covering ~20K genomes). 2. Subset it using gene coordinates (start and end coordinates) and only considering Variants with "PASS,." filter using bcftools 3. Running ka_ks.py on the resulting

dnds kaks VCF

updated 23 days ago • rohitsatyam102

I am using bat (rhinolophus sinicus) snRNA-seq brain samples located [here][1]. The associated paper is located [here][2]. The samples were prepped with the MGI DNBelab C4 scRNA Preparation Kit and were sequenced on the BGI DNBSEQTM technology platform. I downloaded all the bat brain tissue samples with parallel-fastq-dump. Below is an example of downloading a single sample. parallel-fastq-…

STARSolo scRNA-seq STAR snRNA-seq MGI

updated 24 days ago • atowns21

with n_obs × n_vars = 14872 × 36601 obs: 'batch', 'cluster' var: 'Accession', 'Chromosome', 'End', 'Start', 'Strand' obsm: 'X_umap' layers: 'matrix', 'ambiguous', 'spliced', 'unspliced' I generated this object by combining loom files and

loomfile scvelo scipy annData numpy

updated 24 days ago • Kash

herald

updated 25 days ago • Biostar

I created a Seurat object for each one and then merged those 2 Seurat objects together... I just started with scRNA-seq analysis and not sure if this is the correct way to go about it... # Integrate the datasets merged.Seurat

clustering subclustering scRNAseq

updated 25 days ago • alphaflylizard

I am new to the field of bioinformatics and would like to buy a computer for my lab that allows the analysis of several single cell samples, probably

updated 25 days ago • Estevão

I have a large data of virus genome sequences from NCBI but they have internal stop/start codons warning in codonw software due to which i'm not able to analyse them. Since then I've tried using EMBOSS explorer

rscu codonw

updated 25 days ago • SHREYA

I've compiled a table containing DMRs with annotations, including columns such as seqnames start end width strand pvalue qvalue meth.diff annotation geneChr geneStart geneEnd geneLength geneStrand geneId distanceToTSS

rrbs methylkit

updated 25 days ago • Srinka

I need some advice for the new task I have to process. I am new to Bioinformatics and I have to perform QC of the bulk RNAseq data. I have successfully ran Fastqc and multiqc and after seeing

RNA-seq QC Trimmomatic

updated 26 days ago • dxj294

Hello, I am looking for recommendations for bioinformatics tools to perform gene family analysis. I'm currently reviewing CAFE: Computational Analysis of gene Family

Genome gene-family

updated 26 days ago • sansan_96

Hello all, This is probably not a bioinformatics question directly but I am a bioinformatician who has gotten involved with immunology/virology recently...for conferences/ do you have any recommendations for conferences which would also be open for some bioinformatics-based data? So far, I have found: [ECI-2024][1] (I unfortunately missed their submission deadline) and [18th Vaccine

virology conferences immunology

updated 26 days ago • manaswwm

bulk RNA-seq data of tumor samples and matched normal samples. I want to know if there are any bioinformatic tools to detect the somatic variation of tumor samples based on RNA-seq data? Can GATK do this task? Thanks in

RNA-seq variation somatic

updated 26 days ago • feather-W

UK Contract Duration: 2 years (Project based contract) Grading: Grade 6 (Monthly salary starting at £3,456 after tax) + Other paid benefits and allowances based on circumstances Closing Date: 19 May 2024 Reference...researchers, data generators and user communities **You have** - A post-graduate degree in bioinformatics, biology, computer science or a related field or equivalen…

ebi embl genomics ensembl

updated 26 days ago • Ben_Ensembl

Location: EMBL-EBI, Hinxton near Cambridge, UK Contract Duration: 3 years (Grant based contract) Grading: Grade 7 (monthly salary starting at £3,934 after tax) + other paid benefits based on personal circumstances Closing Date: 5 May 2024 Reference Number: EBI02236 [Apply now][1] Ensembl is seeking an enthusiastic Project Leader to join our Outreach team. Ensembl develops free, comprehensi…

ebi embl genomics ensembl

updated 26 days ago • Ben_Ensembl

Hello, I've newly started learning bioinformatics. I wonder how to infer regulons from an expression matrix (row=genes, columns=samples) in R

VIPER MARINA ARACNe

updated 26 days ago • Biostars2200

Hi there I recently start working with some archaic samples (aDNA), specifically two high coverage samples of Neanderthal and Denisova. The latter

samtools bam

updated 27 days ago • Matteo Ungaro

the assembly. I filtered a list of transcripts for primer design, but most of the transcripts do not start with start or stop codons. What factors should I consider for designing primers for those transcripts without start

Primers TRINITY

updated 28 days ago • mathavanbioinfo

Note: I am very new to bioinformatics! I am on a Windows 11 machine using BLAST+ 2.15.0 to run blastp queries against a custom database of shotgun

shotgun metagenomics blastp taxonomy

updated 29 days ago • rebecca.calvo

most the final products have somewhat similar scRNA profile, however I do see variability in the starting material profile. What is the best way to determine the homogeneity and heterogeneity based on cluster frequency...Statistical method to show that the final product is homogeneous irrespective of heterogenous starting material, PCA or cluster frequency. How can I determine the inter and in…

CV PCA scRNA Cluster-Frequency

updated 29 days ago • Nitin

opt/R/4.2.3/bin/R # tell Rstudio which version to use from terminal rstudio # now starting RStudio from the terminal runs R version 4.2.3 (clicking on the desktop icon will still use the default R version

R Ubuntu Linux Bioconductor Rstudio

updated 29 days ago • BioinfGuru

using karyoploteR. My dataset looks like this (with made up examples below): - chromosome number - start: denotes start position of copy number variation - end: denotes the end position of the variation on the chromosome - ploidy...log2_ratio chromosome start end ploidy 1 58865614 58865899 3.512352 2 …

Copy-number-variation genomics

updated 29 days ago • Emmi

of mitochondrial genes compared to other cells after thresholding (10%). Low expression of genes starting with Rmrp, Mrpl, and Mrps. Low expression of ribosomal genes (genes starting with Rpl or Rps). Very high expression of

single-cell

updated 29 days ago • Kazo

I think I run in something of a non-concordant result and I wanted to check out here for some advice. Starting at the SNP calling with ANGSD, I used the following script (notice I changed file names): ``` #!/bin/bash #SBATCH --account my_account...100 \ --min_maf 0.05 \ --n_threads 40 \ --out $OUTDIR/ANGSD_SNPcalls.ld ``` And here is where I start to doubt the process. The output is enormous, p…

lcwgs ngsTools ANGSD genomics

updated 29 days ago • DanielEB_fisk

Hi, I am a beginner in bioinformatics and I would like to learn the basic pipeline for quantifying expression of rna sequences from transcriptomic...gi|126697566|ref|NC_009089.1|:1-1320 0 1320 7904 Basically it tells me the location(start 0, end 1320) and the count (7904). How do I take this data and figure out which exact genes they relate to? I want to get the read

differential-expression transcriptome

updated 4 weeks ago • siddharth.patel.153

test this model on a different dataset. Ideally I should remove the study specific effects before I start. But if you put the new data, together with the old data into `removeBatchEffects` my intution is that the data from study

limma machine-learning batch-effect

updated 4 weeks ago • i.sudbery

Update**: Our manuscript has been published in Bioinformatics -- https://doi.org/10.1093/bioinformatics/btx635. **Abstract**: We propose a data-adaptive, non-parametric, and non

RNA-Seq scRNA-Seq R Batch-Effect

updated 4 weeks ago • Ar

Hi! I'm new at bioinformatics and I'm working with a project where I combine several datasets from GEO. I retrieve the data from GREIN(GEO

Batch-effect transcriptomics

updated 4 weeks ago • BioQueen

12_* **But it gave error;** *-bash-4.2$ ./generate_index.sh Apr 17 10:17:17 ..... started STAR run Apr 17 10:17:17 ... starting to generate Genome files Apr 17 10:21:17 ..... processing annotations GTF Apr 17 10:21:48 ... starting

align RNA-Seq linux STAR

updated 4 weeks ago • n_navy

Hi there, I am wondering how to remove batch effect on segmented_scna data downloading from TCGA PANCANA project. The demo of data format is as following: ``` Sample Chromosome Start End Num_Probes Segment_Mean TCGA-KL-8323-11A-01D-2308-01 1 3218610 104558357 58272 0.0026 TCGA-KL-8323-11A-01D-2308-01...from TCGA PANCANA project. The demo of data format is as following: ``` Sample Chromosome St…

Combat CNA Batch-Effect

updated 4 weeks ago • sugus

Hello there, hope all of you are fine. I do hope you are enjoying this weekend. In my little experience, I always had to deal with samples coming from different batches (i.e. coming from different hospitals or experiments done in different days). One postdoc in my lab showed me how to deal with batch effect by using **SVA package.** I guess it is a brilliant idea to work with that, but if I don'…

RNA-Seq deseq2 batch-effect

updated 4 weeks ago • Mozart

may be due to the overall experimental design. So for an overall background, I was brought on as a bioinformatics analyst after the experiment was ordered and sequenced. From what I know so far there were four experimental

ChIP-Seq batch-effect sequencing

updated 4 weeks ago • dmj6ab

Hello, I am currently working on my master's thesis in bioinformatics (2 weeks in). My tutor has asked me to work with VCF files from ICGC database. Our goal use this data to training

bcftools SnpEff WGS VEP VCF

updated 4 weeks ago • Javier

this experiment? Everything was done before I had any contact with them and I cannot suggest to start everything all over Thanks a lot

statistics protein-array batch-effect

updated 4 weeks ago • s.lima.diogenes

in the strings where the changes can be made. The RNA string do not contain any introns and it start with a start codon and ends with a stop codon. Great thanks in advance

RNA wobble-position R

updated 4 weeks ago • fawazfebin

Hi, I made use of some of the packages for the analysis of the RNA-Seq data starting from the alignment till the expression analysis. This was just for some of the samples from my large datasets, however

RNA-Seq quantification alignment

updated 4 weeks ago • mohammedtoufiq91

I'm working with an Axiom Human Origins Array. The samples have been typed in two separate plates and the PCA is clearly showing the separation between the two batches. I guess I'm facing a batch effect. I'd like to normalize the array data and start over with the work. So far, I've been trying with dChip but it says that the required CDF file I provided is "Not a CDF file or...between the two ba…

affymetrix array batch-effect

updated 4 weeks ago • Simo

Bioinformatics Pipeline Development with Nextflow ------------------------------------------------- *How to manage your own data analysis pipelines using workflow management...Online **Link?** [Website][1] **In a nutshell** - **Learn** the fundamental best-practices of bioinformatic pipeline development - **Understand** how workflow management systems can accelerate your research - **Use**…

workshop RNA-seq nextflow DNA-seq

updated 4 weeks ago • David Langenberger

Hi everyone, I am a student of Biotechonology and I want to learn Bioinformatics. I want to learn mainly the sequencing stuff and data analysis. I do know linux and python and R but I never used...and stuff. Now I was thinking of going to use them for my study but I have no clue where should I start. I tried downloading some raw sequence and used fastqc and multiqc but I had no idea what am I doi…

Sequencing

updated 4 weeks ago • Adi

Hi, I'm new to bioinformatics and I'm analyzing some genomes I obtained from BGI. The average size of these reads is 100bp, but after trimming

Bwa-sampe BGI

updated 4 weeks ago • lorena9132

herald

updated 4 weeks ago • Biostar

to find any thread related to what I want to ask I have decided to create a new post. I recently did start some simple GSE analysis to get a quick overall look at my data results before going more into details and I have trouble

GSEA pathways GO-terms

updated 4 weeks ago • Manko47

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