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13,520 results • Page
2 of 271
Sort: replies
Rank
Views
Votes
Replies
121
votes
35
replies
43k
views
20 follow
Forum:
Snakemake vs. Nextflow: strengths and weaknesses
snakemake
nextflow
updated 11 months ago by
Ram
43k • written 6.9 years ago by
ropolocan
▴ 810
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
36
votes
34
replies
2.8k
views
9 follow
Forum:
New to bioinformatics.....
gene
updated 11 months ago by
Ram
43k • written 6.1 years ago by
sms.00196
• 0
103
votes
34
replies
113k
views
23 follow
How To Split A Bam File By Chromosome
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
GPR
▴ 390
172
votes
34
replies
26k
views
29 follow
Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
r
books
bioconductor
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Michael
54k
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 7 weeks ago by
barslmn
★ 2.1k • written 6.7 years ago by
a.rex
▴ 350
121
votes
33
replies
39k
views
24 follow
Forum:
Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by
carlopecoraro2
★ 2.5k • written 10.7 years ago by
Eric Normandeau
11k
10
votes
33
replies
3.8k
views
Looking for a tool like fastq screen but for ONT data
gridion
nanopore
ont
minion
updated 10 months ago by
Ram
43k • written 5.8 years ago by
Rox
★ 1.4k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
120
votes
31
replies
199k
views
17 follow
Correct Way To Parse A Fasta File In Python
python
fasta
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Eric Normandeau
11k
147
votes
31
replies
137k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 9 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
11
votes
31
replies
14k
views
6 follow
How to concatenate multiple fasta file
sequence
genome
updated 11 months ago by
doggie
• 0 • written 5.7 years ago by
fec2
▴ 50
105
votes
31
replies
94k
views
18 follow
Best Way To Merge A Many Thousand Small Bam Files Into One Big Bam File?
bam
picard
samtools
merge
updated 4 months ago by
mmfansler
▴ 450 • written 12.8 years ago by
2184687-1231-83-
★ 5.1k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Khader Shameer
18k
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Biostar User
★ 1.0k
47
votes
30
replies
4.3k
views
10 follow
Forum:
Bioinformatics software distribution
software
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Petr Ponomarenko
★ 2.8k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 29 days ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 10 months ago by
Ram
43k • written 5.9 years ago by
Jennifer Pham
▴ 450
18
votes
30
replies
10k
views
6 follow
Tool:
Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina
BBMap
filterbytile
updated 10 months ago by
Ram
43k • written 7.3 years ago by
Brian Bushnell
20k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 6 weeks ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
16
votes
29
replies
1.6k
views
Gene labels problem in enhanced volcano
R
ggplot2
enhancedvolcano
updated 11 weeks ago by
Mensur Dlakic
★ 27k • written 12 weeks ago by
anasjamshed
▴ 120
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
4
votes
29
replies
11k
views
6 follow
WGCNA soft thresholding problem
WGCNA
RNA-Seq
soft thresholding
data normalization
updated 8 weeks ago by
foejvs546
▴ 10 • written 5.4 years ago by
catagui
▴ 40
124
votes
29
replies
7.3k
views
18 follow
What License Do You Use When You Release Code And Data?
software
general
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Simon Cockell
7.4k
20
votes
29
replies
2.4k
views
6 follow
Using bcftools to find unique alt homozygous sites
bcftools
updated 6 months ago by
Pierre Lindenbaum
161k • written 6 months ago by
Axzd
▴ 70
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Eric Normandeau
11k
39
votes
28
replies
11k
views
10 follow
How Much Does It Cost To Align A Flowcell In The Cloud?
cloud
12 weeks ago by
Jeremy Leipzig
22k
3
votes
27
replies
2.5k
views
7 follow
Forum:
What server do you use?
HPC
AWS
updated 11 months ago by
Ram
43k • written 5.8 years ago by
caggtaagtat
★ 1.9k
197
votes
27
replies
35k
views
20 follow
Forum:
Bioinformatics Cartoon
bioinformatics
updated 9 months ago by
Ram
43k • written 12.3 years ago by
Maxime Lamontagne
★ 2.3k
26
votes
27
replies
2.0k
views
10 follow
Forum:
Determining computer time required
computer
hpc
time
updated 3 months ago by
dsull
★ 5.8k • written 3 months ago by
Rozita
▴ 40
27
votes
27
replies
10k
views
6 follow
How To Detect And Query Poly-Allelic Snps?
snp
allele
biomart
dbsnp
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Michael
54k
41
votes
27
replies
6.0k
views
8 follow
Forum:
Why bioinformaticians need to know programming languages?
Python
R
Programming
updated 11 months ago by
Ram
43k • written 6.9 years ago by
nilo
▴ 90
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 23 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
28
votes
27
replies
15k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython
python
fastq
next-gen-sequencing
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Darked89
4.6k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 months ago by
snardeli
• 0 • written 10.2 years ago by
Istvan Albert
100k
103
votes
27
replies
89k
views
21 follow
Extract Sub-Set Of Regions From Vcf File
vcf
tabix
genome
filter
updated 11 months ago by
NIRJHAR
• 0 • written 11.9 years ago by
Rubal7
▴ 830
76
votes
26
replies
120k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 5 months ago by
cschu181
★ 2.8k • written 9.0 years ago by
Chenglin
▴ 260
3
votes
26
replies
1.9k
views
6 follow
STAR Genome index Error
STAR
updated 6 months ago by
Ram
43k • written 6 months ago by
Prasanna
• 0
105
votes
26
replies
43k
views
23 follow
How To Create Mutation Diagram In R Or In Any Tools?
mutation
domain
r
updated 7 months ago by
zx8754
11k • written 11.3 years ago by
henryvuong
▴ 810
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 6 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
47
votes
26
replies
4.1k
views
11 follow
Blog:
Evolution of Biostars
meta
Biostars
updated 8 months ago by
aldhairmedico
▴ 70 • written 5.2 years ago by
venu
7.1k
20
votes
26
replies
3.2k
views
Is there a command line tool that can take an alignment fasta and input and outputs an image?
alignment
fasta
image
updated 8 months ago by
Joe
21k • written 4.9 years ago by
Joel Wallenius
▴ 210
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 6 months ago by
Ram
43k • written 14.1 years ago by
User 59
13k
24
votes
26
replies
3.6k
views
Tool:
ClinCNV: CNV detection from short reads
variant-calling
cna
cnv
updated 10 months ago by
Ram
43k • written 4.5 years ago by
German.M.Demidov
★ 2.9k
24
votes
26
replies
2.1k
views
6 follow
Forum:
Organizing a Bioinformatics Conference ?
meeting
conference
updated 11 months ago by
Ram
43k • written 6.4 years ago by
Pierre Lindenbaum
161k
96
votes
26
replies
31k
views
15 follow
What Methods Do You Use For In/Del/Snp Calling?
short-read-aligner
snp
sequencing
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Pierre Lindenbaum
161k
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.2 years ago by
biostart
▴ 370
7
votes
25
replies
10k
views
6 follow
Tool:
MIGEC: towards error-free profiling of immune repertoires
sequencing-error
tcr
antibody
molecular-barcode
updated 10 months ago by
Ram
43k • written 10.0 years ago by
mikhail.shugay
3.5k
69
votes
25
replies
7.0k
views
16 follow
How Do You Explain What You Do To The Guy On The Street Or Your Mum?
general
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Dave Gerrard
▴ 190
51
votes
25
replies
6.9k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Michael
54k
13,520 results • Page
2 of 271
Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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35k
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chaco001
▴ 40
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GenoMax
141k
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Recent Replies
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
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