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
484 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 19 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 11 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
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
26 days ago by
b.contreras.moreira
▴ 170
4
votes
13
replies
880
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 11 days ago by
BioinfGuru
★ 1.7k • written 17 days ago by
matteo.levorato
• 0
3
votes
12
replies
558
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
26 days ago by
Lila M
★ 1.2k
0
votes
11
replies
520
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
2 days ago by
atowns21
• 0
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 11 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 11 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
10
replies
640
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
27 days ago by
dzisis1986
▴ 70
8
votes
10
replies
720
views
bash script
whole-genome-sequencing
updated 13 days ago by
Ram
43k • written 20 days ago by
bestone
▴ 30
4
votes
9
replies
580
views
variant calling
variant-calling
updated 25 days ago by
Ram
43k • written 26 days ago by
dalibenam64
• 0
2
votes
9
replies
846
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 4 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
9
replies
2.4k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
nanopore
basecalling
fastq
updated 2 hours ago by
chujie
• 0 • written 8 months ago by
Gio
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 11 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
595
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 16 days ago by
LauferVA
4.2k • written 18 days ago by
Aki
▴ 20
0
votes
8
replies
335
views
Error in cnetplot enrichplot package
R
updated 6 days ago by
Ram
43k • written 6 days ago by
Farhad
• 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 18 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 19 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
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 11 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 19 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
4
votes
7
replies
571
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 26 days ago by
cmdcolin
★ 3.8k • written 4 weeks ago by
I0110
▴ 140
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 11 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
0
votes
7
replies
328
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
GenoMax
141k • written 6 days ago by
Patadu94
• 0
0
votes
7
replies
408
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 23 days ago by
Papyrus
★ 2.9k • written 24 days ago by
doramora
▴ 10
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 20 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
2
votes
7
replies
831
views
Removing duplicates
duplicates
ONT
minimap2
updated 9 days ago by
noodle
▴ 530 • written 11 days ago by
quentinperriere
• 0
4
votes
7
replies
561
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 14 days ago by
Ram
43k • written 16 days ago by
AHerik
▴ 20
2
votes
6
replies
412
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
20 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 19 days ago by
Ram
43k • written 5.6 years ago by
lkianmehr
▴ 100
0
votes
6
replies
465
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
18 days ago by
marongiu.luigi
▴ 710
2
votes
6
replies
867
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 12 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 19 days ago by
Ram
43k • written 5.8 years ago by
Pin.Bioinf
▴ 340
0
votes
6
replies
616
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 19 days ago by
Ram
43k • written 5 months ago by
tw_140
• 0
4
votes
6
replies
842
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 26 days ago by
Ram
43k • written 5 months ago by
cee28
▴ 30
2
votes
6
replies
639
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 26 days ago by
Ram
43k • written 4 months ago by
zea
• 0
5
votes
6
replies
400
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 26 days ago by
Istvan Albert
100k • written 27 days ago by
Pumla
• 0
0
votes
6
replies
442
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 4 days ago by
gv
• 0 • written 27 days 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 13 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
0
votes
6
replies
557
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
13 days ago by
Dunois
★ 2.5k
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 12 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
5
replies
458
views
Marking duplicates using UMIs
Deduplication
UMI
updated 6 days ago by
i.sudbery
19k • written 7 days ago by
Lipika
• 0
2
votes
5
replies
673
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 23 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 12 days ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
0
votes
5
replies
295
views
How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 24 days ago by
Ram
43k • written 27 days ago by
bioinfo
▴ 150
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing
illumina
updated 19 days ago by
Arup Ghosh
3.2k • written 3.4 years ago by
WhiteN8
• 0
1
vote
5
replies
345
views
samtools filtering
samtools
updated 17 days ago by
jkbonfield
★ 1.2k • written 25 days ago by
sansan_96
▴ 80
0
votes
5
replies
340
views
Incongruencies in GT assignment by Freebayes
depth
freebayes
heterozygous
genotype
23 days ago by
virginia.baraja
• 0
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 18 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
0
votes
5
replies
324
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 1 day ago by
Istvan Albert
100k • written 4 days ago by
sehriban.buyukkilic
▴ 10
2
votes
5
replies
468
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
11 days ago by
Bikram Kumar
• 0
484 results • Page
1 of 10
Recent Votes
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
Answer: How to use limma to find differentially expressed genes in response to a continu
Batch effects : ComBat or removebatcheffects (limma package) ?
Recent Locations •
All
Berlin,
1 minute ago
Moscow,
2 minutes ago
United States,
3 minutes ago
Germany,
3 minutes ago
Warsaw,
5 minutes ago
USA,
5 minutes ago
United States,
8 minutes ago
Recent Awards •
All
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
rj.rezwan
• 0
Popular Question
to
husensofteng
▴ 410
Popular Question
to
Raheleh
▴ 260
Popular Question
to
Aspire
▴ 300
Popular Question
to
rene.j.erhardt
▴ 20
Popular Question
to
yueli7
▴ 250
Recent Replies
Answer: NGS forensics: how to know if data is fabricated
by
Mensur Dlakic
★ 27k
I share the opinion by @philippbayer I have seen enough questionable things in life and in science to keep me permanently jaded, but there…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I downloaded the data in two files from the link you provided. With this command: megahit -1 ERR072246_1.fastq.gz -2 ERR072246_2.fastq…
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
If you have Linux the assembly should work on your system, but 8 GB is generally not enough for assembling larger genomes.
Comment: How many reads for WGS Sequencing?
by
Mensur Dlakic
★ 27k
I think you might be getting stuck on less relevant parts of my exercise. The most important point was that nothing is wrong with the data.…
Comment: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
Great comprehensive explanation and overview of the technologies -- with regards to sequencing assays, the one thing I'd add is SNV identif…
Answer: What does it mean single base resolution in sequencing?
by
dsull
★ 5.9k
I think that term means slightly different things in different contexts. For example, it's useful to profile mRNA modifications (e.g. m6a) …
Comment: Cannot process all the reads in a fast5 file?
by
chujie
• 0
Hi, I met the same problem, have you found the solution?
Answer: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
Hi @fe3e6f65 , In a single sentence, the answer to your question can be summarized as, "*the resolution of a genomic technology refers to …
Comment: PCA plot
by
LauferVA
4.2k
Without more context, we cannot interpret this PCA plot. There are many possibilities. In addition, this question is basic enough that it w…
Comment: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
i have the name ready: out**liar**
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
Sequencing by hybridization (https://en.wikipedia.org/wiki/Sequencing_by_hybridization ) is likely not giving you single base resolution. B…
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
Hii... i have updated the script in python..But, still getting no data found. Actually the data is there, i have print the parsed html file…
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
Comment: Downloading full alignments from Pfam
by
GenoMax
141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing?
by
GenoMax
141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Traffic: 1826 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