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
515 results • Page
4 of 11
Sort: replies
Rank
Views
Votes
Replies
0
votes
2
replies
371
views
I can't add VAF from population for all of my variants from VCF file
vaf
vcf
genomics
gnomad
allelicfrequency
26 days ago by
Samuel
▴ 20
0
votes
2
replies
220
views
BLASTP short sequences (<20aa) - interpreting results
blast
sequence
blastp
alignment
16 days ago by
neish
• 0
0
votes
2
replies
171
views
Highest variable features in single cell data
single-cell
updated 23 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
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
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 9 days ago by
Ram
43k • written 4.4 years ago by
akutasame
▴ 40
0
votes
2
replies
224
views
Bedmethyl file format
bedmethyl
methylation
updated 9 days ago by
GenoMax
141k • written 9 days ago by
njornet
▴ 20
0
votes
2
replies
209
views
utr sequence retrieval from UCSC
UTR
SEQUENCING
UCSC
GENOME
updated 23 days ago by
GenoMax
141k • written 23 days ago by
kim
▴ 70
0
votes
2
replies
268
views
How to get genes in a gene set in msigdb?
msigdb
21 days ago by
Chris
▴ 260
0
votes
2
replies
872
views
freebayes calls presumably homozygous variants as heterozygotes
SNP
freebayes
variant-call
genotyping
updated 21 days ago by
virginia.baraja
• 0 • written 3.1 years ago by
johanna.pieplow
• 0
0
votes
2
replies
273
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
13 days ago by
ramin.k2013
• 0
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
0
votes
2
replies
222
views
Annovar using R package
Annovar
gnomAD
R
23 hours ago by
DKA
▴ 40
1
vote
2
replies
219
views
convert a seurat object to expressionset
Seurat
15 days ago by
Bine
▴ 60
1
vote
2
replies
287
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
10 days ago by
bp22
▴ 80
0
votes
2
replies
222
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
14 days ago by
marongiu.luigi
▴ 710
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 8 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
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
2
replies
316
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 11 days ago by
Istvan Albert
100k • written 12 days ago by
Jiang
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 9 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
3
votes
2
replies
241
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
29 days ago by
DYLAN NICO
• 0
0
votes
2
replies
237
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 2 days ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
3
votes
2
replies
301
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Single-Cell
updated 21 days ago by
Ram
43k • written 8 weeks ago by
Daddy
▴ 20
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
7 days ago by
Ashok
• 0
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 6 weeks ago by
geocarvalho
▴ 360
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 8 days ago by
Ram
43k • written 6.6 years ago by
Alternative
▴ 270
0
votes
2
replies
218
views
RNA-Seq isoforms identification
RNA-seq
updated 23 days ago by
Andres
▴ 20 • written 23 days ago by
latita.atun
• 0
1
vote
2
replies
202
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
1
vote
2
replies
1.0k
views
An issue with application of SPAdes genome assembly in Galaxy
Galaxy
SPAdes
updated 24 days ago by
Ram
43k • written 2.4 years ago by
adnan.lahuf
• 0
0
votes
2
replies
513
views
Gene expression assay Yeast sample prep
Live-cells
updated 24 days ago by
Ram
43k • written 22 months ago by
dshdixit
▴ 10
0
votes
2
replies
266
views
Regions not clear in VCF
whole-exome
variant-calling
updated 18 days ago by
Ram
43k • written 19 days ago by
priya.bmg
▴ 60
1
vote
2
replies
202
views
In need of help with my RNA velocity trajectory inference pipeline!
RNAvelocity
18 days ago by
phhelou5
• 0
0
votes
2
replies
247
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
9 days ago by
DKA
▴ 40
1
vote
2
replies
274
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 9 days ago by
Ram
43k • written 9 days ago by
aniigodwinn
• 0
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
234
views
permutation test in edgeR
rna-seq
edgeR
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 18 days ago by
Netanel
• 0
1
vote
2
replies
626
views
Nanopore multisample variant calling
SNPs
nanopore
SNP-calling
variants
multisample
28 days ago by
colindaven
6.4k
0
votes
2
replies
317
views
GSEA analysis in R
GSEA
R
Arabidopsis
8 days ago by
Sudip
• 0
0
votes
2
replies
246
views
Problem with downloading genome in SnpEff
SnpEff
16 days ago by
Javier
• 0
0
votes
2
replies
249
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
9 days ago by
mropri
▴ 150
1
vote
2
replies
219
views
PCA plot
DESeq2
PCAplot
updated 11 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
2
replies
264
views
RNAseq 1 control 2 different treatment
RNA-seq
10 days ago by
matteo.levorato
• 0
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
0
votes
2
replies
578
views
Bacterial contamination in human DNA sample
Long-read-sequencing
Bacterial-contamination
updated 21 days ago by
Ram
43k • written 22 months ago by
priya.bmg
▴ 60
0
votes
2
replies
244
views
Cell communacations analysis. I only have the proteome of one type of cell
How
to
updated 23 days ago by
QX
• 0 • written 4 weeks ago by
David Arturo
• 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
2
votes
2
replies
273
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 15 days ago by
ATpoint
82k • written 15 days ago by
Shicheng Guo
★ 9.4k
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
7 days ago by
Ashok
• 0
0
votes
2
replies
261
views
bam merging for archaic samples
samtools
bam
updated 5 days ago by
Ram
43k • written 6 days ago by
Matteo Ungaro
▴ 100
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 21 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
0
votes
2
replies
316
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
13 days ago by
O.rka
▴ 710
515 results • Page
4 of 11
Recent Votes
Comment: PCA plot
C: RNA seq library size
RNA seq library size
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
Recent Locations •
All
United States,
1 minute ago
United States,
2 minutes ago
UCLA,
4 minutes ago
Stony Brook University, NY,
4 minutes ago
USA,
5 minutes ago
United States,
5 minutes ago
Spain,
13 minutes ago
Recent Awards •
All
Popular Question
to
chaco001
▴ 40
Commentator
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
Recent Replies
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 :(
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…
Traffic: 2575 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