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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
1
vote
8
replies
682
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 17 days ago by
Anand Rao
▴ 630 • written 7 weeks ago by
bvm
▴ 20
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 9 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 23 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
1
vote
8
replies
3.3k
views
cutadapt error problem
next-gen
cutadapt
updated 29 days ago by
Ram
43k • written 5.6 years ago by
amitpande74
▴ 20
0
votes
8
replies
538
views
FreeBayes encountered a sudden error
freebayes
updated 21 days ago by
Michael
54k • written 22 days ago by
emilydolivo97
▴ 10
7
votes
8
replies
667
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
22 days ago by
Riq
▴ 50
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat
RNA-Seq
Limma
DESeq2
batch-effect
updated 8 days ago by
Ram
43k • written 4.9 years ago by
borkk
▴ 140
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 10 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 1 day ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
0
votes
7
replies
303
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 11 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
7
votes
7
replies
1.2k
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 11 days ago by
Dunois
★ 2.5k • written 12 days ago by
AdviceSeeker
• 0
4
votes
7
replies
593
views
UK biobank versus Genomics England
WGS
DRAGEN
GenomicsEngland
UK-BRAP
vcf
written 12 weeks ago by
zizigolu
★ 4.3k
4
votes
7
replies
553
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 13 days ago by
Ram
43k • written 14 days ago by
AHerik
▴ 20
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 17 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 10 days ago by
Дана
• 0 • written 6 months ago by
Lukas
▴ 50
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 22 days ago by
Vassilis
• 0 • written 10.1 years ago by
liu4gre
▴ 210
3
votes
7
replies
520
views
Artificial deletion in bam
bam
updated 21 days ago by
Zhenyu Zhang
★ 1.2k • written 22 days ago by
enee
▴ 10
3
votes
7
replies
459
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
10 days ago by
ntsopoul
▴ 60
3
votes
7
replies
962
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 22 days ago by
Ram
43k • written 5 months ago by
bioinfo
▴ 150
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 18 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 9 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
0
votes
7
replies
651
views
Help with summarizeOverlaps function in RNASeq analysis using R
R
RNA-Seq
summarizeOverlaps
GenomicAlignments
updated 19 days ago by
BioinfGuru
★ 1.7k • written 28 days ago by
FJCF
• 0
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
1
vote
7
replies
437
views
fastp - can I trim specific adapters only?
trimming
fastp
adapter
15 days ago by
liorglic
★ 1.4k
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering
dendrogram
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 4.0 years ago by
Ankit
▴ 500
0
votes
7
replies
402
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 21 days ago by
Papyrus
★ 2.9k • written 22 days ago by
doramora
▴ 10
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab
benchmark
fastq
wgs
data-access
updated 24 days ago by
geocarvalho
▴ 360 • written 5.1 years ago by
Fungsten
• 0
0
votes
7
replies
476
views
Selection criteria for nanobody
Nanobody
updated 25 days ago by
LChart
3.9k • written 25 days ago by
farahnazir2
• 0
2
votes
7
replies
511
views
STARsolo ; Reads are NOT mapped to transcriptome
STARsolo
updated 15 days ago by
GenoMax
141k • written 17 days ago by
gdfsnkfns
• 0
4
votes
7
replies
566
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 24 days ago by
cmdcolin
★ 3.8k • written 28 days ago by
I0110
▴ 140
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 7 days ago by
ATpoint
82k • written 7.2 years ago by
boymin2020
▴ 80
4
votes
7
replies
421
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 1 day ago by
dsull
★ 5.8k • written 2 days ago by
VITALA
• 0
1
vote
7
replies
467
views
Installing Cell Ranger
cellranger
24 days ago by
gdfsnkfns
• 0
7
votes
7
replies
551
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 14 days ago by
Matthias Zepper
4.5k • written 14 days ago by
4fzcgueyp5
• 0
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake
ngs
updated 10 days ago by
进
• 0 • written 3.9 years ago by
Peter Chung
▴ 200
2
votes
7
replies
820
views
Removing duplicates
duplicates
ONT
minimap2
updated 8 days ago by
joe
▴ 510 • written 9 days ago by
quentinperriere
• 0
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 15 days ago by
kaaz
• 0 • written 5.6 years ago by
ste.lu
▴ 80
1
vote
7
replies
5.1k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python
seaborn
updated 16 days ago by
Wubin
▴ 40 • written 3.4 years ago by
roy.granit
▴ 880
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
2
votes
6
replies
513
views
Correcting coordinates in gff3 file
awk
unix
gff3
python
updated 14 days ago by
Matthias Zepper
4.5k • written 16 days ago by
hulu
• 0
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 10 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
1
vote
6
replies
419
views
Rename multiple fastq.gz files
fastq
next-gen
updated 10 days ago by
shenwei356
8.4k • written 10 days ago by
Jérémie
• 0
2
votes
6
replies
574
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
22 days ago by
Lissa Cruz Saavedra
• 0
2
votes
6
replies
404
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
18 days ago by
jkim
▴ 170
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 8 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 9 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
6
votes
6
replies
4.4k
views
10x to cloupe
single-cell-transcriptomics
10x
17 days ago by
firestar
★ 1.6k
1
vote
6
replies
2.1k
views
DGE on protein-coding and lncRNAs separately?
differential-gene-expression
RNA-seq
updated 17 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 17 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 8 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
1,000 results • Page
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A: Blast Settings For Short Sequences
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Answer: A faidx-indexed FASTA format file or a FASTA format file
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Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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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…
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Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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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…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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Please include a link when you are recommending a tool. There can be programs with similar names.
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Check out clustergrammer from Avi Ma'ayan's lab.
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43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
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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)…
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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…
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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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sapuizait
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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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