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1,000 results • Page
2 of 20
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 6.8 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 10 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
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 6 weeks ago by
barslmn
★ 2.1k • written 6.7 years ago by
a.rex
▴ 350
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
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
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
147
votes
31
replies
137k
views
26 follow
Useful Bash Commands To Handle Fasta Files
command-line
fasta
bash
updated 8 months ago by
Ram
43k • written 12.2 years ago by
Anima Mundi
★ 2.9k
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
120
votes
31
replies
198k
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
11
votes
31
replies
14k
views
6 follow
How to concatenate multiple fasta file
sequence
genome
updated 10 months ago by
doggie
• 0 • written 5.7 years ago by
fec2
▴ 50
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 5 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
102
votes
30
replies
62k
views
25 follow
Tools To Find Gene Ontology Term Enrichment
gene
enrichment
updated 5 months ago by
Ram
43k • written 14.1 years ago by
Biostar User
★ 1.0k
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 22 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
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
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
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
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 5 weeks ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
4
votes
29
replies
11k
views
6 follow
WGCNA soft thresholding problem
WGCNA
RNA-Seq
soft thresholding
data normalization
updated 7 weeks ago by
foejvs546
▴ 10 • written 5.4 years ago by
catagui
▴ 40
16
votes
29
replies
1.6k
views
Gene labels problem in enhanced volcano
R
ggplot2
enhancedvolcano
updated 10 weeks ago by
Mensur Dlakic
★ 27k • written 11 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
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
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
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 5 months ago by
Ram
43k • written 14.0 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
11 weeks ago by
Jeremy Leipzig
22k
197
votes
27
replies
34k
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
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
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 16 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
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
103
votes
27
replies
88k
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
41
votes
27
replies
5.9k
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
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
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
76
votes
26
replies
120k
views
15 follow
How to count fastq reads
sequence
next-gen
fastq
reads
updated 4 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
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 5 months ago by
Ram
43k • written 14.1 years ago by
User 59
13k
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 5 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
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
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
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
38
votes
26
replies
18k
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
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
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 14.0 years ago by
Pierre Lindenbaum
161k
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
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
38
votes
25
replies
9.1k
views
13 follow
FASTA file of fixed length
sequence
fasta
updated 7 months ago by
Ram
43k • written 8.0 years ago by
waqasnayab
▴ 250
1,000 results • Page
2 of 20
Recent Votes
Answer: Cellranger count error: Input FASTQ file ended prematurely
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
Answer: Illumina Read Stitching
Answer: Problem with Sniffles pipeline and SV calling help
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Popular Question
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Rodolfo Adrián
• 0
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damian.szk
▴ 70
Popular Question
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alphaflylizard
• 0
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GenoMax
141k
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161k
Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
GenoMax
141k
You may also want to note at beginning that this is targeted for linux (may work on macOS?).
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
BioinfGuru
★ 1.7k
Thanks @Ram I'll add that to the intro. I'm the admin on my machine so I haven't found it necessary to install any other way. I'll try a fr…
Comment: Downloading the raw microarray data from GEO
by
GenoMax
141k
No GPR files with this data unless you ask the submitters for them directly. You can find the matrix of data here: https://ftp.ncbi.nlm.nih…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
GenoMax
141k
That is odd. Thanks for following-up and providing an explanation.
Answer: Cellranger count error: Input FASTQ file ended prematurely
by
bp22
▴ 70
Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
by
Ram
43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately?
by
Ram
43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis
by
BioinfGuru
★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
by
Mohamed Abderrahmane
▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications
by
Enrique
• 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster?
by
ATpoint
81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis
by
joe
▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort
by
ATpoint
81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files
by
Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
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