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379 results • Page
3 of 8
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Views
Votes
Replies
2
votes
2
replies
8.2k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 4 months ago by
Ram
40k • written 5.8 years ago by
chen
★ 2.4k
81
votes
8
replies
8.2k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 6 months ago by
Ram
40k • written 9.3 years ago by
Malachi Griffith
19k
14
votes
0
replies
8.1k
views
Tutorial:
Video: ChIP-Seq Analysis and Visualization using Galaxy and IGB.
IGB
ChIP-Seq
Galaxy
MACS
RNA-Seq
updated 18 months ago by
Ram
40k • written 8.7 years ago by
Nowlan Freese
▴ 860
18
votes
22
replies
8.1k
views
10 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 7 days ago by
evoecogen
▴ 20 • written 3.8 years ago by
Juke34
8.2k
8
votes
7
replies
8.0k
views
Tutorial:
Getting Cegma/Genewise To Work On Centos, Rhel
centos
genewise
rhel
cegma
updated 20 months ago by
Ram
40k • written 9.8 years ago by
Adrian Pelin
★ 2.6k
12
votes
5
replies
7.9k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 5 months ago by
Ram
40k • written 7.3 years ago by
Shicheng Guo
★ 9.3k
0
votes
0
replies
7.8k
views
Tutorial:
Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R
eviews
updated 4 months ago by
Ram
40k • written 5.7 years ago by
helgasaraswati
▴ 10
16
votes
11
replies
7.7k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
6 months ago by
Ram
40k
6
votes
1
reply
7.7k
views
Tutorial:
Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat
RNA-seq
cufflinks
updated 7 months ago by
Ram
40k • written 11.4 years ago by
Istvan Albert
98k
20
votes
2
replies
7.6k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 4 months ago by
Ram
40k • written 5.9 years ago by
bernatgel
★ 3.4k
12
votes
0
replies
7.5k
views
Tutorial:
Plot average methylation levels across TSS region
bedtools
RRBS
R
methylation
updated 17 months ago by
Ram
40k • written 8.7 years ago by
TriS
★ 4.7k
42
votes
19
replies
7.4k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 7 months ago by
Ram
40k • written 10.6 years ago by
Daniel Standage
4.1k
50
votes
1
reply
7.4k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 7 months ago by
Ram
40k • written 3.0 years ago by
ATpoint
77k
6
votes
4
replies
7.2k
views
Tutorial:
Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization
ChIP-seq
RNA-seq
ucsc-genome-browser
bigwig
updated 7 months ago by
Ram
40k • written 10.5 years ago by
Sukhi Singh
11k
26
votes
17
replies
7.1k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 12 months ago by
Ram
40k • written 9.1 years ago by
Ian
6.0k
60
votes
2
replies
7.1k
views
Tutorial:
Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
32
votes
4
replies
7.1k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 6 months ago by
Ram
40k • written 4.9 years ago by
firestar
★ 1.6k
4
votes
2
replies
7.0k
views
Tutorial:
Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink
gwas
updated 7 months ago by
Ram
40k • written 11.4 years ago by
Istvan Albert
98k
64
votes
5
replies
7.0k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
next-gen
RNA-Seq
updated 11 months ago by
Ram
40k • written 8.2 years ago by
GouthamAtla
12k
12
votes
11
replies
7.0k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 4 months ago by
Ram
40k • written 6.6 years ago by
CandiceChuDVM
★ 2.4k
24
votes
4
replies
6.9k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 6 months ago by
Ram
40k • written 4.1 years ago by
ATpoint
77k
19
votes
13
replies
6.8k
views
9 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 23 hours ago by
dariober
14k • written 15 months ago by
ATpoint
77k
15
votes
1
reply
6.7k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 4 months ago by
Ram
40k • written 5.9 years ago by
Joseph Hughes
★ 3.0k
15
votes
2
replies
6.7k
views
Tutorial:
Genotype And Snp Calling Review Papers
snp
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
2
votes
0
replies
6.6k
views
Tutorial:
How to - Install Python packages in a virtual environment (virtualenv)
ubuntu
cutadapt
virtualenv
python
windows
updated 4 months ago by
Ram
40k • written 5.8 years ago by
vimalkvn
▴ 310
5
votes
5
replies
6.5k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 4 months ago by
Ram
40k • written 5.9 years ago by
jmzeng1314
▴ 130
16
votes
0
replies
6.5k
views
Tutorial:
Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course
training
updated 7 months ago by
Ram
40k • written 11.3 years ago by
Istvan Albert
98k
20
votes
5
replies
6.5k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 5 months ago by
Ram
40k • written 7.3 years ago by
Geparada
★ 1.5k
8
votes
2
replies
6.4k
views
Tutorial:
Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics
clinical-genomics
updated 20 months ago by
Ram
40k • written 8.9 years ago by
GouthamAtla
12k
8
votes
12
replies
6.4k
views
Tutorial:
Create your own VPN to access work resources from home
tinyproxy
OpenVPN
VPN
updated 5 months ago by
Ram
40k • written 7.3 years ago by
John
13k
14
votes
2
replies
6.3k
views
Tutorial:
ChIP-seq analysis tutorial
ChIP-Seq
updated 6 months ago by
Ram
40k • written 8.1 years ago by
Ming Tommy Tang
★ 3.4k
21
votes
9
replies
6.3k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 7 months ago by
Ram
40k • written 10.3 years ago by
Medhat
9.7k
6
votes
0
replies
6.2k
views
Tutorial:
Leveraging Flow Order And Flow Signals From Ion Torrent Data
ion-torrent
updated 7 months ago by
Ram
40k • written 11.4 years ago by
Biostar User
▴ 360
23
votes
19
replies
6.2k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 5 months ago by
Ram
40k • written 7.0 years ago by
chen
★ 2.4k
29
votes
5
replies
6.1k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 7 months ago by
Ram
40k • written 10.0 years ago by
ole.tange
★ 4.3k
16
votes
6
replies
6.1k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 5 months ago by
Ram
40k • written 6.9 years ago by
Botond Sipos
★ 1.7k
21
votes
10
replies
6.0k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 6 months ago by
Ram
40k • written 3.1 years ago by
rpolicastro
12k
20
votes
7
replies
6.0k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 6 months ago by
Ram
40k • written 5.0 years ago by
ahmad mousavi
▴ 760
4
votes
1
reply
6.0k
views
Tutorial:
Chip-Seq Data Analysis Tutorial
chip-seq
updated 7 months ago by
Ram
40k • written 11.4 years ago by
Biostar User
▴ 360
14
votes
7
replies
5.9k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 6 months ago by
Ram
40k • written 7.4 years ago by
steve
★ 3.3k
16
votes
9
replies
5.8k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 15 months ago by
dk0319
▴ 70 • written 22 months ago by
Barry Digby
★ 1.2k
36
votes
5
replies
5.8k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 22 days ago by
gallardodiazmiriam
▴ 20 • written 8.2 years ago by
Luke Crichton
▴ 410
34
votes
15
replies
5.8k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by
Ram
40k • written 4.3 years ago by
Shicheng Guo
★ 9.3k
11
votes
0
replies
5.8k
views
Tutorial:
Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 6 months ago by
Ram
40k • written 2.7 years ago by
GenoMax
134k
22
votes
2
replies
5.8k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 5 months ago by
Ram
40k • written 6.9 years ago by
Eric Lim
★ 2.1k
13
votes
31
replies
5.7k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 6 months ago by
Ram
40k • written 4.1 years ago by
Juke34
8.2k
18
votes
7
replies
5.7k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 10 weeks ago by
ATpoint
77k • written 3.5 years ago by
colindaven
5.5k
18
votes
2
replies
5.7k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 4 months ago by
Ram
40k • written 6.4 years ago by
Sej Modha
5.2k
13
votes
6
replies
5.6k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 5 months ago by
Ram
40k • written 7.3 years ago by
dariober
14k
6
votes
3
replies
5.5k
views
Tutorial:
High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 7 months ago by
Ram
40k • written 11.2 years ago by
Istvan Albert
98k
379 results • Page
3 of 8
Recent Votes
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
• 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output
by
langziv
▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
by
Pierre Lindenbaum
157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data
by
fifty_fifty
▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
• 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names?
by
Joseph
• 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
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