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318 results • Page 2 of 7
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Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
32
votes
12
replies
29k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 9 months ago by 41k • written 10.1 years ago by 99k
8
votes
12
replies
6.5k
views
Tutorial: Create your own VPN to access work resources from home
tinyproxy OpenVPN VPN
updated 7 months ago by 41k • written 7.5 years ago by 13k
12
votes
11
replies
7.1k
views
Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI Bioproject SRA BioSample
updated 6 months ago by 41k • written 6.7 years ago by ★ 2.4k
16
votes
11
replies
7.9k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
8 months ago by Ram 41k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 8 months ago by 41k • written 7.1 years ago by ★ 4.7k
6
votes
11
replies
5.3k
views
6 follow
Tutorial: Add count numbers to headers in a fasta file
genome
updated 9 months ago by 41k • written 7.0 years ago by ▴ 50
21
votes
10
replies
6.3k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 8 months ago by 41k • written 3.2 years ago by 12k
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 8 months ago by 41k • written 2.7 years ago by ★ 1.5k
6
votes
10
replies
5.0k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 8 months ago by 41k • written 5.8 years ago by ▴ 370
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 9 months ago by 41k • written 10.4 years ago by ★ 3.0k
9
votes
9
replies
4.0k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 6 months ago by 41k • written 6.2 years ago by 86k
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 9 months ago by 41k • written 9.6 years ago by ★ 1.8k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 9 months ago by 41k • written 9.6 years ago by ★ 1.9k
21
votes
9
replies
6.3k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
7
votes
8
replies
3.3k
views
Tutorial: Determine if a transcription factor is bound with CENTIPEDE
ChIP-Seq transcription-factor DNase-Seq CENTIPEDE
updated 11 months ago by 41k • written 8.4 years ago by ★ 2.2k
81
votes
8
replies
8.3k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 9 months ago by 41k • written 9.5 years ago by 19k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 9 months ago by 41k • written 9.6 years ago by ▴ 810
99
votes
8
replies
28k
views
8 follow
Tutorial: Guide to TCGA data
cancer RNA-Seq clinical TCGA
updated 8 months ago by 41k • written 7.8 years ago by ★ 1.1k
20
votes
7
replies
6.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 8 months ago by 41k • written 5.1 years ago by ▴ 770
18
votes
7
replies
6.0k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 4 months ago by 78k • written 3.7 years ago by 5.7k
11
votes
7
replies
9.9k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.7 years ago by ▴ 360
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
16
votes
7
replies
15k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 8 months ago by 41k • written 4.5 years ago by ▴ 310
11
votes
7
replies
1.9k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 months ago by barslmn ★ 2.0k
14
votes
7
replies
6.1k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 8 months ago by 41k • written 7.5 years ago by ★ 3.4k
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 6 months ago by 41k • written 6.2 years ago by 86k
13
votes
7
replies
5.6k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 8 months ago by 41k • written 3.2 years ago by 86k
39
votes
6
replies
18k
views
Tutorial: Creating chromosome karyotype plot with R and ggplot2
ggplot2 R chromosome karyotype
updated 6 months ago by 41k • written 6.3 years ago by ★ 3.4k
2
votes
6
replies
3.0k
views
Tutorial: Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene R Rembrandt
updated 7 months ago by 41k • written 7.4 years ago by ▴ 140
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.5 years ago by 86k
16
votes
6
replies
6.2k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 7 months ago by 41k • written 7.1 years ago by ★ 1.7k
20
votes
6
replies
5.3k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 8 months ago by 41k • written 7.2 years ago by ★ 5.2k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 8 months ago by 41k • written 5.2 years ago by 16k
13
votes
6
replies
5.7k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 7 months ago by 41k • written 7.5 years ago by 14k
67
votes
6
replies
25k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.8 years ago by 6.0k
61
votes
6
replies
9.3k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by 41k • written 10.3 years ago by 9.7k
5
votes
5
replies
6.7k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 6 months ago by 41k • written 6.1 years ago by ▴ 130
12
votes
5
replies
2.2k
views
Tutorial: FASTA file split
fasta
updated 8 months ago by 41k • written 3.5 years ago by 8.4k
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 7 months ago by 41k • written 7.5 years ago by 20k
21
votes
5
replies
6.6k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 7 months ago by 41k • written 7.4 years ago by ★ 1.5k
2
votes
5
replies
2.1k
views
Tutorial: Building OMA database on SGE
oma
updated 7 months ago by 41k • written 7.4 years ago by ▴ 10
12
votes
5
replies
8.1k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 7 months ago by 41k • written 7.5 years ago by ★ 9.3k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 8 months ago by 41k • written 6.0 years ago by ▴ 770
10
votes
5
replies
21k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 8 months ago by 41k • written 5.4 years ago by ★ 9.3k
29
votes
5
replies
6.2k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 9 months ago by 41k • written 10.2 years ago by ★ 4.4k
9
votes
5
replies
2.1k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 6 months ago by 41k • written 6.4 years ago by 99k
16
votes
5
replies
8.8k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 9 months ago by 41k • written 11.2 years ago by 20k
318 results • Page 2 of 7
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Popular Question to endre.sebestyen ▴ 10
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Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters? by AMARU • 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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