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75
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14
replies
15k
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15 follow
Tutorial: List Of Bioinformatics Books
books
updated 10 months ago by 41k • written 10.6 years ago by 9.7k
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 weeks ago by ▴ 50 • written 3.3 years ago by ▴ 160
20
votes
14
replies
3.7k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization Windows EaSeq
updated 8 months ago by 41k • written 7.6 years ago by ▴ 460
7
votes
14
replies
3.2k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 13 months ago by • 0 • written 21 months ago by ▴ 30
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 9 months ago by 41k • written 10.8 years ago by 6.0k
19
votes
13
replies
8.0k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 4 weeks ago by • 0 • written 17 months ago by 78k
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
75
votes
13
replies
66k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 13 months ago by 41k • written 10.0 years ago by ★ 1.2k
17
votes
13
replies
2.0k
views
Tutorial: Screen shots of text (please don't)!
meta
updated 6 months ago by 41k • written 6.7 years ago by 53k
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 22 months ago by 41k • written 9.1 years ago by ★ 2.4k
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.1 years ago by 41k • written 9.5 years ago by 19k
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.1 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 8 months ago by 41k • written 7.5 years ago by 13k
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
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
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 7 months ago by 41k • written 6.7 years ago by ★ 2.4k
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 10 months ago by 41k • written 7.0 years ago by ▴ 50
29
votes
10
replies
73k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 9 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
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 3.3 years ago by 12k
65
votes
9
replies
48k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 10 months ago by 41k • written 10.4 years ago by ★ 3.0k
16
votes
9
replies
6.2k
views
Tutorial: TCGA transcriptome data to R (DESeq2)
TCGA GDC DESeq2
updated 18 months ago by ▴ 70 • written 2.0 years ago by ★ 1.3k
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
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
21
votes
9
replies
6.4k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
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 9.7 years ago by ★ 1.9k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 9 months ago by 41k • written 3.2 years ago by 3.1k
23
votes
8
replies
5.2k
views
Tutorial: A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K methylation
updated 23 months ago by 41k • written 9.3 years ago by 24k
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 9.7 years ago by ▴ 810
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 12 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
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
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
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
8
votes
7
replies
8.1k
views
Tutorial: Getting Cegma/Genewise To Work On Centos, Rhel
centos genewise rhel cegma
updated 22 months ago by 41k • written 10.0 years ago by ★ 2.6k
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 2.8 years ago by ▴ 360
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
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 7.6 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
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
19
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 5.8k
30
votes
6
replies
22k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 14 months ago by 41k • written 11.6 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 9.9 years ago by 6.0k
44
votes
6
replies
23k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 22 months ago by ▴ 40 • written 2.7 years ago by 12k
11
votes
6
replies
4.8k
views
Tutorial: sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 16 months ago by 41k • written 7.8 years ago by ★ 4.2k
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
13
votes
6
replies
5.7k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 8 months ago by 41k • written 7.5 years ago by 14k
16
votes
6
replies
6.2k
views
Tutorial: How to make your snakefiles self-documenting
snakemake
updated 8 months ago by 41k • written 7.1 years ago by ★ 1.7k
384 results • Page 2 of 8
Recent Votes
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
Answer: Calculate GC content for entire chromosome
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
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Recent Replies
Comment: vcftools by sevda • 0
Hello, Thank you for your attention. It ran successfully and I got no errors or warnings but no new files were created.
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
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