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412 results • Page 5 of 9
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Tutorial: How to ask computational biology questions
computational-biology
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
4
votes
2
replies
2.5k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 14 months ago by 43k • written 4.9 years ago by ★ 9.4k
1
vote
2
replies
3.3k
views
Tutorial: Standalone BLAST error: UnexpectedTagClassByte
software-error blast
updated 19 months ago by 43k • written 8.8 years ago by ▴ 10
4
votes
2
replies
3.6k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 14 months ago by 43k • written 8.2 years ago by ★ 2.5k
8
votes
2
replies
1.2k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 9 months ago by 43k • written 9 months ago by ★ 2.5k
15
votes
2
replies
2.1k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 19 months ago by ▴ 830 • written 2.7 years ago by ▴ 360
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 15 months ago by 43k • written 12.1 years ago by ▴ 540
0
votes
2
replies
2.4k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 13 months ago by 43k • written 7.7 years ago by ▴ 190
4
votes
2
replies
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
7
votes
2
replies
3.6k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 15 months ago by 43k • written 11.6 years ago by 11k
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by 43k • written 7.1 years ago by ▴ 650
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
3
votes
2
replies
5.3k
views
Tutorial: Reorder Vcf Files
vcf
updated 14 months ago by 43k • written 11.0 years ago by ▴ 60
23
votes
2
replies
5.9k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 20 months ago by ▴ 40 • written 3.1 years ago by 8.6k
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 12 months ago by 43k • written 7.1 years ago by ▴ 30
7
votes
2
replies
2.0k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.8 years ago by ▴ 90
6
votes
2
replies
4.2k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 12 months ago by 43k • written 7.0 years ago by ★ 1.6k
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
10 months ago by Ming Tommy Tang ★ 3.9k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.1k
5
votes
2
replies
2.3k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 14 months ago by 43k • written 5.3 years ago by ▴ 10
3
votes
2
replies
8.9k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 12 months ago by 43k • written 6.5 years ago by ★ 2.5k
7
votes
2
replies
1.8k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 13 months ago by 43k • written 7.7 years ago by ★ 3.9k
18
votes
2
replies
10k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.2 years ago by 43k • written 9.6 years ago by ▴ 860
10
votes
2
replies
3.5k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 21 months ago by 43k • written 8.5 years ago by 20k
5
votes
2
replies
2.3k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 14 months ago by 43k • written 5.5 years ago by ▴ 50
15
votes
1
reply
7.2k
views
Tutorial: A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl SAM blast BED
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.0k
6
votes
1
reply
2.6k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 14 months ago by 43k • written 9.5 years ago by 9.7k
4
votes
1
reply
3.2k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 15 months ago by 43k • written 12.0 years ago by ▴ 360
1
vote
1
reply
1.4k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 14 months ago by 43k • written 3.8 years ago by • 0
0
votes
1
reply
585
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
12
votes
1
reply
5.1k
views
Tutorial: RepSeq data processing and analysis
immunology tcr repseq sequencing repertoire
updated 19 months ago by 43k • written 8.8 years ago by 3.5k
0
votes
1
reply
314
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 43k • written 4 months ago by ▴ 120
11
votes
1
reply
2.7k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 14 months ago by 43k • written 3.4 years ago by ★ 27k
3
votes
1
reply
3.8k
views
Tutorial: Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene R
updated 13 months ago by 43k • written 7.9 years ago by ▴ 140
50
votes
1
reply
8.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 15 months ago by 43k • written 3.7 years ago by 82k
7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 12 months ago by 43k • written 6.6 years ago by ★ 1.7k
15
votes
1
reply
3.2k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 13 months ago by 43k • written 8.0 years ago by 20k
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 12 months ago by 43k • written 6.9 years ago by ★ 1.6k
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
8
votes
1
reply
1.9k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 14 months ago by 43k • written 8.9 years ago by ▴ 430
2
votes
1
reply
62k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 22 months ago by 4.2k • written 22 months ago by ▴ 20
3
votes
1
reply
658
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.6k
2
votes
1
reply
3.0k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 19 months ago by 43k • written 8.7 years ago by ★ 1.1k
1
vote
1
reply
379
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 43k • written 4 months ago by ▴ 120
10
votes
1
reply
9.3k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 12 months ago by 43k • written 6.7 years ago by ▴ 110
0
votes
1
reply
1.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 14 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Tutorial: Guide Tutorial DEAP 2.1 In Windows 7
DEAP2.1 R stata
updated 14 months ago by 43k • written 6.4 years ago by ▴ 10
2
votes
1
reply
1.6k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 14 months ago by 43k • written 4.0 years ago by ★ 2.5k
10
votes
1
reply
2.3k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 14 months ago by 43k • written 4.1 years ago by ★ 2.5k
6
votes
1
reply
7.8k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 15 months ago by 43k • written 12.0 years ago by 100k
412 results • Page 5 of 9
Recent Votes
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Recent Replies
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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