Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this month
all time
today
this week
this month
this year
514 results • Page
2 of 11
Sort: Votes
Rank
Views
Votes
Replies
2
votes
12
replies
740
views
Nanopore data filtering using fastp
fastp
nanopore
29 days ago by
emilydolivo97
▴ 10
2
votes
4
replies
293
views
Addmetadata to seurat obj
seurat
16 days ago by
synat.keam
▴ 100
2
votes
10
replies
824
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 29 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
2
votes
2
replies
261
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
10 days ago by
bioinfo
▴ 150
2
votes
9
replies
822
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
7
replies
815
views
Removing duplicates
duplicates
ONT
minimap2
updated 7 days ago by
joe
▴ 510 • written 9 days ago by
quentinperriere
• 0
2
votes
3
replies
254
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics
RNA-Seq
p-value
updated 24 days ago by
Ram
43k • written 24 days ago by
Netanel
• 0
2
votes
2
replies
273
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 14 days ago by
ATpoint
82k • written 15 days ago by
Shicheng Guo
★ 9.4k
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
24 days ago by
b.contreras.moreira
▴ 170
2
votes
5
replies
669
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 21 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
2
votes
1
reply
281
views
Forgot the web site with comparison of NGS platforms
NGS
platforms
updated 27 days ago by
cmdcolin
★ 3.8k • written 27 days ago by
konstantinkul
▴ 110
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 9 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
5
replies
685
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 5 days ago by
Jesse
▴ 740 • written 6 days ago by
Ann
★ 2.4k
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 8 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 9 days ago by
Ram
43k • written 3.5 years ago by
chatterjee.arumoy
▴ 50
2
votes
2
replies
630
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 9 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma
Batch-effect
MDS
Galaxy
updated 9 days ago by
Ram
43k • written 4.8 years ago by
sonayuv
• 0
1
vote
3
replies
209
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
0
replies
539
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
6 days ago by
mathavanbioinfo
▴ 90
1
vote
0
replies
88
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
1 day ago by
rohitsatyam102
▴ 850
1
vote
2
replies
210
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 29 days ago by
Ram
43k • written 29 days ago by
gdfsnkfns
• 0
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 9 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca
ruvseq
sva
svaseq
batch-effect
updated 9 days ago by
Ram
43k • written 6.2 years ago by
jjrin
▴ 40
1
vote
4
replies
389
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 13 days ago by
BioinfGuru
★ 1.7k • written 14 days ago by
Morteza
• 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 9 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
1
reply
175
views
Failed to download data from EBI with ascp
EBI
aspera
updated 15 days ago by
GenoMax
141k • written 15 days ago by
biock
▴ 60
1
vote
2
replies
287
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
10 days ago by
bp22
▴ 80
1
vote
1
reply
414
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 5 days ago by
Gordon Smyth
★ 7.0k • written 8 days ago by
Chris
▴ 260
1
vote
1
reply
462
views
PLINK multivariable GLM output: p-value without BETA and SE
linear-model
glm
plink
updated 18 days ago by
chrchang523
10k • written 18 days ago by
dsbusiness135
▴ 10
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 9 days ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
1
vote
4
replies
812
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing
wgs
16 days ago by
Hyper_Odin
▴ 310
1
vote
2
replies
327
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 23 days ago by
jkbonfield
★ 1.2k • written 5 weeks ago by
geocarvalho
▴ 360
1
vote
2
replies
808
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 9 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
1
vote
4
replies
280
views
Removing batch effect using combat-seq
batch
effect
RNA-Seq
combat-seq
updated 24 days ago by
BioinfGuru
★ 1.7k • written 25 days ago by
Netanel
• 0
1
vote
5
replies
269
views
Downsampling fastq file
downsample
fastq
updated 4 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 80
1
vote
3
replies
250
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
1
vote
1
reply
225
views
Retrieve a % coverage for each transcript
RNA-seq
updated 9 days ago by
Ram
43k • written 9 days ago by
jammydodger123456
▴ 40
1
vote
0
replies
368
views
Differential expression analysis on multiple integrated datasets
microarray
Z-score
limma
differential-gene-expression
meta-analysis
updated 17 days ago by
Ram
43k • written 2.4 years ago by
michael.s
▴ 10
1
vote
3
replies
351
views
how to do the repeatability filtering of vcf files?
snp
vcf.
updated 25 days ago by
Pierre Lindenbaum
161k • written 26 days ago by
Max
• 0
1
vote
1
reply
412
views
Long reads Annotation
long-reads
pacbio
updated 21 days ago by
Ram
43k • written 2.1 years ago by
Gerardo
• 0
1
vote
2
replies
267
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
9 days ago by
bioinfo
▴ 150
1
vote
2
replies
923
views
vg surject for long reads
long-reads
vg
variation-graph
surject
updated 21 days ago by
Ram
43k • written 23 months ago by
ved_vyas
▴ 10
1
vote
2
replies
315
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 10 days ago by
Istvan Albert
100k • written 12 days ago by
Jiang
• 0
1
vote
2
replies
821
views
Replacing default numbers with geneNames in enhancedVolcano
EnhancedVolcano
updated 24 days ago by
Ram
43k • written 2.6 years ago by
Mohan
• 0
1
vote
3
replies
347
views
Ensembl gene id conversion
biomart
ensembl
updated 10 days ago by
ATpoint
82k • written 12 days ago by
naveedhasan2000
• 0
1
vote
0
replies
155
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 15 days ago by
Ram
43k • written 15 days ago by
ian.will
▴ 30
1
vote
0
replies
53
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
11 hours ago by
KABILAN
▴ 50
1
vote
3
replies
255
views
CCA with random effects model
CCA
updated 24 days ago by
dariober
14k • written 24 days ago by
leranwangcs
▴ 120
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 7 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
514 results • Page
2 of 11
Recent Votes
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
Answer: Should I use unpaired reads from trimmomatic
A: Mean Variance Relationship single cell RNA-Seq Data
Answer: Blasting two protein sequences vs two nucleotide sequences
Recent Locations •
All
UCLA,
1 minute ago
United States,
1 minute ago
Brazil,
1 minute ago
United States,
2 minutes ago
Sweden,
3 minutes ago
Stony Brook University, NY,
4 minutes ago
Brazil,
6 minutes ago
Recent Awards •
All
Scholar
to
GenoMax
141k
Popular Question
to
rheab1230
▴ 140
Popular Question
to
BioinfGuru
★ 1.7k
Scholar
to
bk11
★ 2.4k
Popular Question
to
vinayjrao
▴ 250
Supporter
to
Jalil Sharif
▴ 80
Popular Question
to
sil_bioinfo
▴ 40
Recent Replies
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 :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Traffic: 4037 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6