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319 results • Page 4 of 7
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5
votes
3
replies
4.1k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 9 months ago by 41k • written 11.0 years ago by ▴ 80
6
votes
2
replies
4.0k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
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
6
votes
2
replies
3.7k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 8 months ago by 41k • written 7.7 years ago by ▴ 840
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
3
votes
2
replies
3.7k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 6 months ago by 41k • written 6.7 years ago by ▴ 30
3
votes
1
reply
3.6k
views
Tutorial: Importance of Array Quality Control - arrayQualityMetrics (PART I)
gene R
updated 8 months ago by 41k • written 7.5 years ago by ▴ 140
15
votes
2
replies
3.6k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
10
votes
2
replies
3.6k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 6 months ago by 41k • written 6.7 years ago by 26k
6
votes
0
replies
3.5k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 9 months ago by 41k • written 9.5 years ago by 8.1k
3
votes
0
replies
3.5k
views
Tutorial: Video Tutorial On Conducting Whole-Exome Sequencing Research
exome-sequencing
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
3
votes
4
replies
3.5k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 6 months ago by 41k • written 5.1 years ago by ▴ 340
0
votes
0
replies
3.5k
views
Tutorial: Park Test for Heteroskedasticity In R Commander
R Park-Test
updated 6 months ago by 41k • written 5.9 years ago by ▴ 10
0
votes
0
replies
3.5k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 6 months ago by 41k • written 5.8 years ago by ▴ 10
4
votes
2
replies
3.5k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 8 months ago by 41k • written 7.8 years ago by ★ 2.5k
7
votes
2
replies
3.5k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 9 months ago by 41k • written 11.2 years ago by 11k
10
votes
4
replies
3.4k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 months ago by 41k • written 5.8 years ago by 86k
3
votes
0
replies
3.4k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 9 months ago by 41k • written 3.4 years ago by 8.4k
6
votes
0
replies
3.3k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
9 months ago by Novogene ▴ 360
19
votes
2
replies
3.3k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 6 months ago by 41k • written 6.7 years ago by ▴ 640
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
1
vote
4
replies
3.2k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 6 months ago by 41k • written 5.6 years ago by ▴ 340
1
vote
4
replies
3.2k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 8 months ago by 41k • written 7.5 years ago by ▴ 10
4
votes
1
reply
3.1k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 9 months ago by 41k • written 11.6 years ago by ▴ 360
2
votes
0
replies
3.1k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 5 months ago by 41k • written 6.1 years ago by ★ 2.5k
22
votes
1
reply
3.1k
views
Tutorial: Introduction To R Course Materials Available
R
updated 11 months ago by 41k • written 11.6 years ago by 26k
5
votes
0
replies
3.1k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 8 months ago by 41k • written 3.8 years ago by ★ 3.4k
6
votes
0
replies
3.1k
views
Tutorial: Uc Riverside Bioinformatics Manuals
computing-manuals
updated 9 months ago by 41k • written 11.6 years ago by 26k
15
votes
1
reply
3.1k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 8 months ago by 41k • written 7.6 years ago by 19k
1
vote
3
replies
3.1k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 8 months ago by 41k • written 7.3 years ago by ▴ 300
0
votes
1
reply
3.0k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 6 months ago by 41k • written 6.1 years ago by • 0
0
votes
0
replies
3.0k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
5
votes
2
replies
3.0k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 6 months ago by 41k • written 6.6 years ago by ★ 9.3k
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 8 months ago by 41k • written 7.4 years ago by ▴ 140
2
votes
1
reply
3.0k
views
Tutorial: How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools SNP-Filtering VCF
updated 8 months ago by 41k • written 3.8 years ago by ▴ 10
7
votes
0
replies
3.0k
views
Tutorial: On the concept of constant or intercept used in Differential Expression (DE) analysis
regression limma DESeq2
updated 8 months ago by 41k • written 7.6 years ago by ★ 5.1k
6
votes
1
reply
2.9k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 9 months ago by 41k • written 9.6 years ago by ▴ 220
15
votes
2
replies
2.9k
views
Tutorial: Introduction to bedtools.
bedtools
updated 9 months ago by 41k • written 9.1 years ago by 12k
2
votes
0
replies
2.9k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 4 months ago by 41k • written 4 months ago by ★ 3.6k
0
votes
1
reply
2.8k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 8 months ago by 41k • written 5.3 years ago by ▴ 320
0
votes
0
replies
2.8k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 6 months ago by 41k • written 6.0 years ago by ▴ 10
12
votes
17
replies
2.6k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa
updated 11 months ago by 41k • written 8.5 years ago by 99k
0
votes
1
reply
2.6k
views
Tutorial: Clustering and results Display from PART II (PART III) - MeV software version
gene R
updated 8 months ago by 41k • written 7.5 years ago by ▴ 140
6
votes
2
replies
2.6k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 9 months ago by 41k • written 9.8 years ago by ▴ 610
2
votes
3
replies
2.6k
views
Tutorial: It's about the journey, and not the destination
R network
updated 6 months ago by 41k • written 6.7 years ago by ★ 1.2k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 8 months ago by 41k • written 2.9 years ago by ★ 25k
12
votes
0
replies
2.5k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 8 months ago by 41k • written 3.3 years ago by 12k
3
votes
2
replies
2.5k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
4
votes
2
replies
2.5k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 3 months ago by 136k • written 3.6 years ago by 78k
20
votes
4
replies
2.5k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 8 months ago by 41k • written 4.6 years ago by ▴ 180
319 results • Page 4 of 7
Recent Votes
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?
A: Extract somatic mutations and germline mutations from variant calling files?
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Popular Question to samreen.jasvi • 0
Teacher to h.mon 35k
Scholar to jared.andrews07 ★ 16k
Popular Question to Mr Locuace ▴ 150
Popular Question to benjamin.pyenson • 0
Popular Question to Malachi Griffith 19k
Popular Question to awhale01 • 0
Recent Replies
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%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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