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13,523 results • Page
2 of 271
Sort: Views
Rank
Views
Votes
Replies
48
votes
9
replies
44k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 12 weeks ago by
Picasa
▴ 640 • written 7.5 years ago by
ZheFrench
▴ 570
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
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
81
votes
21
replies
42k
views
15 follow
How To Get Bed File Containing Exons Of Canonical Transcripts And Their Corresponding Gene Symbols
bed
transcript
ucsc
biomart
updated 7 months ago by
Joel Wallenius
▴ 210 • written 10.2 years ago by
pristanna
▴ 750
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 9 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing
fastq
updated 5 months ago by
Pierre Lindenbaum
161k • written 14.0 years ago by
Zach Stednick
▴ 660
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
6
votes
25
replies
38k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 11 months ago by
13554221497
• 0 • written 6.1 years ago by
ARich
▴ 130
23
votes
4
replies
38k
views
bcftools compressing and indexing vcf files
sequence
bcftools
vcf
index
updated 5 months ago by
GenoMax
141k • written 5.6 years ago by
Inquisitive8995
▴ 270
19
votes
10
replies
38k
views
Ensembl ID to Gene Symbol
gene-symbol
updated 10 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
27
votes
21
replies
38k
views
12 follow
Converting a VCF with SNPs and indels to BED format
next-gen
updated 6 months ago by
Axzd
▴ 70 • written 9.8 years ago by
onter
▴ 170
13
votes
6
replies
37k
views
generating genome indexes with STAR
RNA-Seq
STAR
updated 9 months ago by
DareDevil
★ 4.3k • written 7.8 years ago by
snp87
▴ 80
10
votes
5
replies
37k
views
How to compare 2 VCF files
vcf
SNP
updated 10 months ago by
Ram
43k • written 10.0 years ago by
Parimala Devi
▴ 100
80
votes
21
replies
37k
views
17 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 5 months ago by
kathryn.jacksonjones
• 0 • written 10.0 years ago by
M K
▴ 660
21
votes
8
replies
37k
views
8 follow
Merging/Concatenating Vcf Files
vcftools
snp
indel
updated 8 months ago by
Bioinformatics_NewComer
▴ 330 • written 11.7 years ago by
bioinfo
▴ 830
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq
macs
ChIP-Seq
peaks
updated 10 months ago by
Ram
43k • written 7.7 years ago by
igor
13k
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing
duplicates
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Pierre Lindenbaum
161k
33
votes
10
replies
35k
views
8 follow
Convert between RefSeq and Ensembl Transcript?
refseq
ensembl
updated 9 months ago by
Ram
43k • written 9.8 years ago by
pwg46
▴ 540
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
20
votes
10
replies
34k
views
6 follow
read depth using samtools
depth
samtools
updated 7 months ago by
Sachin
▴ 10 • written 5.3 years ago by
LimMo
▴ 30
13
votes
12
replies
34k
views
Estimating Insert Size From Paired End Data.
picard
alignment
paired-end
updated 7 months ago by
Ram
43k • written 10.2 years ago by
GouthamAtla
12k
39
votes
23
replies
34k
views
11 follow
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
bcftools
updated 7 months ago by
s.w.vanderlaan
▴ 40 • written 2.8 years ago by
Michal Nevo
▴ 130
28
votes
11
replies
34k
views
10 follow
Samtools View: Only Forward Or Reverse Strand
samtools
strand
updated 3 months ago by
shaoqian ma
• 0 • written 12.4 years ago by
Gregor Rot
▴ 540
42
votes
16
replies
34k
views
14 follow
Generating consensus sequence from bam file
genome
samtools
bwa
fasta
updated 7 months ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
chparada
▴ 70
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline
next-gen-sequencing
rna
rna-seq
updated 11 months ago by
Ram
43k • written 13.9 years ago by
brentp
24k
298
votes
122
replies
33k
views
29 follow
Mean Length Of Fasta Sequences
code
fasta
sequence
codegolf
updated 7 months ago by
jena
▴ 290 • written 13.8 years ago by
Eric Normandeau
11k
78
votes
38
replies
33k
views
15 follow
Illumina Instrument Type from fastq?
fastq
updated 8 weeks ago by
nickp60
▴ 60 • written 7.8 years ago by
andrew.j.skelton73
6.5k
36
votes
11
replies
33k
views
6 follow
Sjdboverhang Option In Star
updated 9 months ago by
Kermit
▴ 90 • written 10.2 years ago by
Martombo
★ 3.1k
36
votes
25
replies
32k
views
15 follow
Downsampling dataset with more than 60 million reads
next-gen
RNA-Seq
updated 4 months ago by
asalimih
▴ 60 • written 9.7 years ago by
mike
▴ 90
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter
sequence
human
genome
updated 5 months ago by
Ram
43k • written 14.0 years ago by
Yuri
★ 1.7k
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
9
replies
32k
views
8 follow
Biomart Bioconductor - Retrieving All Entrezgenes Of Hsapiens_Gene_Ensembl
biomart
r
bioconductor
updated 11 months ago by
Kevin Blighe
87k • written 11.8 years ago by
sthait
▴ 120
185
votes
45
replies
32k
views
27 follow
How To Organize A Pipeline Of Small Scripts Together?
pipeline
general
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Giovanni M Dall'Olio
28k
79
votes
86
replies
31k
views
20 follow
Tool:
Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify
storage
bbmap
pigz
compression
updated 10 months ago by
Ram
43k • written 7.4 years ago by
Brian Bushnell
20k
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
72
votes
71
replies
31k
views
17 follow
Tool:
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot
bioconductor
ggplot2
ggrepel
updated 10 months ago by
Ram
43k • written 5.7 years ago by
Kevin Blighe
87k
14
votes
8
replies
31k
views
NarrowPeak format of ChiP-seq
ChIP-Seq
tag-density
updated 10 months ago by
minakshiboruahassam
• 0 • written 9.9 years ago by
liu4gre
▴ 210
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 18 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
28
votes
16
replies
31k
views
11 follow
How Do I Convert From Bed Format To Gff Format?
gff
galaxy
bed
updated 6 months ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
130
votes
19
replies
31k
views
9 follow
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
RNA-Seq
alignment
next-gen
R
assembly
updated 3 months ago by
Ram
43k • written 4.6 years ago by
WUSCHEL
▴ 750
4
votes
9
replies
31k
views
8 follow
How To Get Chromosome Position Given Rs Number?
snp
chromosome
position
updated 5 months ago by
GenoMax
141k • written 10.4 years ago by
chrismas05
• 0
23
votes
12
replies
30k
views
9 follow
Extract Alignment From Very Large Bam File
bam
updated 3 months ago by
Ram
43k • written 11.9 years ago by
Plantae
▴ 390
25
votes
11
replies
30k
views
9 follow
Bed For Agilent Sureselect All Exon Kits ?
bed
exome
agilent
next-gen
written 11.4 years ago by
Pierre Lindenbaum
161k
31
votes
23
replies
30k
views
15 follow
Amino Acid Change To Genomic Location
snp
amino-acids
updated 3 months ago by
gernophil
▴ 80 • written 12.3 years ago by
Preethi
▴ 110
54
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer
annotation
classification
updated 9 months ago by
DareDevil
★ 4.3k • written 10.8 years ago by
user
▴ 940
13
votes
3
replies
29k
views
What is the difference between blastx and tblastn?
assembly
blast
ncbi
sequence
updated 11 months ago by
Ram
43k • written 4.9 years ago by
Kumar
▴ 120
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 21 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
19
votes
9
replies
28k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis
RNA-Seq
ngs
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Arindam Ghosh
▴ 510
13,523 results • Page
2 of 271
Recent Votes
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
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: Create a new bed file with all pairwise combinations between two other bed files
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Recent Replies
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…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
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