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
477 results • Page
1 of 10
Sort: replies
Rank
Views
Votes
Replies
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 23 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 16 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 15 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
4
votes
13
replies
928
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 16 days ago by
BioinfGuru
★ 1.7k • written 21 days ago by
matteo.levorato
• 0
0
votes
11
replies
578
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
7 days ago by
atowns21
• 0
8
votes
10
replies
753
views
bash script
whole-genome-sequencing
updated 17 days ago by
Ram
43k • written 25 days ago by
bestone
▴ 30
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 16 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
0
votes
10
replies
491
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 10 days ago by
Patadu94
• 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 15 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 16 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
2
votes
9
replies
867
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 9 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
3 days ago by
anna
▴ 20
4
votes
9
replies
596
views
variant calling
variant-calling
updated 29 days ago by
Ram
43k • written 4 weeks ago by
dalibenam64
• 0
0
votes
9
replies
617
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 21 days ago by
LauferVA
4.2k • written 22 days ago by
Aki
▴ 20
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 4 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 15 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 17 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
1
vote
8
replies
445
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 23 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 23 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
8
replies
365
views
Error in cnetplot enrichplot package
R
updated 10 days ago by
Ram
43k • written 10 days ago by
Farhad
• 0
3
votes
7
replies
325
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
3 days ago by
salias
• 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 23 days ago by
Ram
43k • written 6.5 years ago by
vikram
▴ 10
0
votes
7
replies
6.1k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 16 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
0
votes
7
replies
419
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 28 days ago by
Papyrus
★ 2.9k • written 29 days ago by
doramora
▴ 10
2
votes
7
replies
891
views
Removing duplicates
duplicates
ONT
minimap2
updated 14 days ago by
noodle
▴ 580 • written 16 days ago by
quentinperriere
• 0
4
votes
7
replies
582
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 19 days ago by
Ram
43k • written 20 days ago by
AHerik
▴ 20
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 24 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
0
votes
6
replies
585
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
17 days ago by
Dunois
★ 2.5k
2
votes
6
replies
254
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
11 hours ago by
Qroid
▴ 40
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 3 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
0
votes
6
replies
484
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
23 days ago by
marongiu.luigi
▴ 710
2
votes
6
replies
878
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 16 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2
RNA-Seq
Differential-gene-Expression
updated 23 days ago by
Ram
43k • written 5.8 years ago by
Pin.Bioinf
▴ 340
0
votes
6
replies
463
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 9 days ago by
gv
• 0 • written 4 weeks ago by
Srinka
▴ 20
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 17 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
2
votes
6
replies
434
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
24 days ago by
jkim
▴ 170
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 23 days ago by
Ram
43k • written 5.6 years ago by
lkianmehr
▴ 100
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 16 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
6
replies
620
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 23 days ago by
Ram
43k • written 5 months ago by
tw_140
• 0
0
votes
5
replies
365
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 5 days ago by
Istvan Albert
100k • written 9 days ago by
sehriban.buyukkilic
▴ 10
0
votes
5
replies
342
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
0
votes
5
replies
347
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 28 days ago by
GenoMax
142k • written 28 days ago by
Sony
▴ 10
2
votes
5
replies
929
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 3 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
1
vote
5
replies
356
views
samtools filtering
samtools
updated 22 days ago by
jkbonfield
★ 1.2k • written 29 days ago by
sansan_96
▴ 80
0
votes
5
replies
417
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 22 days ago by
GenoMax
142k • written 23 days ago by
Shay
• 0
0
votes
5
replies
349
views
Incongruencies in GT assignment by Freebayes
depth
freebayes
heterozygous
genotype
27 days ago by
virginia.baraja
• 0
2
votes
5
replies
480
views
Marking duplicates using UMIs
Deduplication
UMI
updated 11 days ago by
i.sudbery
19k • written 12 days ago by
Lipika
• 0
2
votes
5
replies
520
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
16 days ago by
Bikram Kumar
• 0
0
votes
5
replies
568
views
seg fault, core dumped with manta 1.6.0
manta
gdb
updated 24 days ago by
Ram
43k • written 28 days ago by
Greg
• 0
477 results • Page
1 of 10
Recent Votes
Convert vcf files with phased genotypes to standard haplotype format
Convert vcf files with phased genotypes to standard haplotype format
A: Convert vcf files with phased genotypes to standard haplotype format
How to extract haplotype data from phased bcf files
How to extract haplotype data from phased bcf files
Answer: RNA-seq data for deep learning classification
Answer: Analysis of intronic reads included scRNA-seq data
Recent Locations •
All
Istanbul, Turkey,
just now
Sweden,
1 minute ago
United Kingdom,
1 minute ago
Sheffield, UK,
1 minute ago
UK,
2 minutes ago
France,
2 minutes ago
United Kingdom,
2 minutes ago
Recent Awards •
All
Scholar
to
eebloom
▴ 80
Popular Question
to
ManuelDB
▴ 80
Popular Question
to
rustykb
▴ 20
Popular Question
to
sativus
▴ 20
Student
to
Mariana
▴ 40
Popular Question
to
kuttibiotech2009
▴ 30
Popular Question
to
analyst
▴ 30
Recent Replies
Comment: RNA-seq data for deep learning classification
by
Yuju
• 0
Thank you very much for sharing your advice. Yes, it definitely makes sense that with the use of deep learning, models would learn normalis…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I didn't use the same tool as in the paper...
Comment: read length in structural variant calling
by
eebloom
▴ 80
Yes good idea. I guess the quality of the SV calls and as a proxy for quality the length and distribution of variants called might be infor…
Comment: Generating mpileup file using samtools
by
Ruqaiya
• 0
I just realised I didn't align my reads with the tools they used and used bowtie2 instead. I can't download the older version that is menti…
Comment: Downsampling long-read BAM files
by
eebloom
▴ 80
This is not what I needed for this particular use case, as capping the coverage would lose the information on regions of copy number amplif…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Apologies, I deleted the question as I wasn't sure it would be helpful to others and it didn't seem to have a clear answer, not to snub the…
Comment: Do I need to go back and filter my long-reads?
by
eebloom
▴ 80
Thanks, I think it would be a good idea to track the results downstream to look for batch effects. I think I will filter the reads ultimate…
Comment: Generating mpileup file using samtools
by
ATpoint
82k
Seconding this. Apply current best practices (which is bcftools mpileup followed by something I forgot, see bcftools manual for variant cal…
Answer: Analysis of intronic reads included scRNA-seq data
by
ATpoint
82k
By default in CellRanger (lets assume you have 10x data processed with it) intronic reads are included. What you get in your matrix.mtx fil…
Comment: How does gene length effect the number of reads mapped
by
i.sudbery
19k
The number of reads for a gene is almost exactly linearly proportional to the length of the gene. In paired-end sequencing, we generally co…
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
ATpoint
82k
Can you post your setup, so how many groups and their replication number? I can tell you by experience that you need even more replication …
Answer: DSEQ2 analysis
by
ATpoint
82k
The tool is called D**E**Seq2. Anyway, if your factor is `factor(conditions, levels = c("control", "mutant"))` then the first level is the …
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Traffic: 2229 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