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
1,000 results • Page
6 of 20
Sort: Votes
Rank
Views
Votes
Replies
3
votes
3
replies
723
views
KissDE and batch effect
kissDE
kissplice
7 days ago by
david.b.rombaut
▴ 10
2
votes
1
reply
223
views
Finding orthologs between genome error
OMA
OMAbrowser
updated 4 days ago by
Adrian Altenhoff
★ 1.1k • written 4 days ago by
hemantcnaik
• 0
2
votes
5
replies
674
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 23 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
2
votes
5
replies
2.2k
views
Generating a heatmap in DEG analysis
Differential-gene-expression
RNA-Seq
updated 19 days ago by
Ram
43k • written 3.1 years ago by
Pranathi
▴ 10
2
votes
5
replies
477
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
12 days ago by
Bikram Kumar
• 0
2
votes
6
replies
609
views
Hybrid assembly Pacbio- Nanopore
long-reads
hybric
assembly
genome
short-reads
24 days ago by
Lissa Cruz Saavedra
• 0
2
votes
4
replies
6.1k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 10 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
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 10 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
2
votes
3
replies
319
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
emmanouil.a
▴ 120
2
votes
7
replies
5.7k
views
8 follow
How to access specifically 30x NA12878 sequencing runs
giab
benchmark
fastq
wgs
data-access
updated 26 days ago by
geocarvalho
▴ 360 • written 5.1 years ago by
Fungsten
• 0
2
votes
5
replies
307
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
6 hours ago by
analyst
▴ 30
2
votes
1
reply
864
views
Multiple BAM files (ccs) input with Lima (PacBio)
Long-read-sequencing
PacBio
updated 23 days ago by
Ram
43k • written 2.8 years ago by
aa9gj
▴ 10
2
votes
3
replies
391
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 13 days ago by
ATpoint
82k • written 15 days ago by
IM
• 0
2
votes
4
replies
1.2k
views
PLINK p value returning NA
GWAS
PLINK
updated 20 days ago by
chrchang523
10k • written 18 months ago by
Sin Yu, Lin
• 0
2
votes
9
replies
850
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 5 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
2
replies
278
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 17 days ago by
ATpoint
82k • written 17 days ago by
Shicheng Guo
★ 9.4k
2
votes
5
replies
461
views
Marking duplicates using UMIs
Deduplication
UMI
updated 7 days ago by
i.sudbery
19k • written 8 days ago by
Lipika
• 0
2
votes
0
replies
211
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
14 days ago by
Alexander
▴ 220
2
votes
4
replies
267
views
filtering VCF sites and impose whatever excluded ad missing
conditions
vcf
filters
bcftools
25 days ago by
Matteo Ungaro
▴ 100
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 12 days ago by
Ram
43k • written 3.5 years ago by
chatterjee.arumoy
▴ 50
2
votes
3
replies
932
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 13 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
2
votes
1
reply
295
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 9 days ago by
GenoMax
141k • written 9 days ago by
rebecca.calvo
• 0
2
votes
3
replies
1.1k
views
Polishing PACBIO corrected assembly using ONT and ILLUMINA data (.fastq)
fasta
Nanopore
long-read
fastq
updated 23 days ago by
Ram
43k • written 2.9 years ago by
K
▴ 10
2
votes
2
replies
299
views
Creating a cytoscape bubble figure
cytoscape
network
GO
17 days ago by
Dave Carlson
★ 1.7k
2
votes
1
reply
285
views
Forgot the web site with comparison of NGS platforms
NGS
platforms
updated 29 days ago by
cmdcolin
★ 3.8k • written 4 weeks ago by
konstantinkul
▴ 110
2
votes
6
replies
465
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
17 days ago by
sansan_96
▴ 80
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 10 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
2
votes
1
reply
169
views
multiple reference sequences
freebayes
updated 26 days ago by
GenoMax
141k • written 27 days ago by
emilydolivo97
▴ 10
2
votes
5
replies
316
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
3 days ago by
Lada
▴ 30
2
votes
5
replies
703
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 8 days ago by
Jesse
▴ 740 • written 9 days ago by
Ann
★ 2.4k
2
votes
4
replies
375
views
How to I use prefetch (SRAtoolkit) on multiple accessions all at one?
sratoolkit
prefetch
updated 22 days ago by
Pierre Lindenbaum
161k • written 22 days ago by
biotrekker
▴ 100
2
votes
4
replies
307
views
I am unsure why my files are not being accepted in bedtools jaccard, any tips?
bedtools
26 days ago by
Ronin
• 0
2
votes
4
replies
323
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
5 days ago by
HyperEvo
• 0
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads
RNA-seq
gene-expression
read-count
updated 23 days ago by
Ram
43k • written 2.9 years ago by
gat
• 0
2
votes
2
replies
249
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 12 days ago by
bk11
★ 2.4k • written 12 days ago by
bgbs
• 0
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat
RNA-Seq
batch-effect
sva
updated 11 days ago by
Ram
43k • written 4.8 years ago by
Shaway
• 0
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 12 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 12 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 11 days ago by
Ram
43k • written 5.9 years ago by
Poorya Parvizi
▴ 60
2
votes
5
replies
1.0k
views
Ties in reranked list
fgsea
GSEA
updated 15 days ago by
Gordon
• 0 • written 7 months ago by
Hamza
• 0
2
votes
5
replies
489
views
Creating an index from multiple .fsa files
HISAT2
BWA
Alignment
20 days ago by
theworldsagainstme
• 0
2
votes
3
replies
337
views
Read Classification from ONT
classification
reads
nanopore
updated 23 days ago by
dthorbur
★ 1.9k • written 24 days ago by
maevalefeuvre
• 0
2
votes
1
reply
958
views
How to evaluate the performance of an RNA-seq pipeline
Differential-gene-expression
RNA-Seq
R
DESeq2
updated 19 days ago by
Ram
43k • written 4.0 years ago by
nhaus
▴ 310
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 7 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 10 days ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
2
votes
4
replies
379
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 14 days ago by
GenoMax
141k • written 14 days ago by
Sony
▴ 10
2
votes
3
replies
957
views
Method to detect genome doubling
CNV
genome doubling
updated 6 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
4
replies
326
views
SnpEff annotates coding duplication as intronic?
snpeff
12 days ago by
kirill.zaslavsky
• 0
2
votes
1
reply
304
views
How to highlight genes on genome visual reprezentation/what tool to use?
gene
genome
updated 15 days ago by
Alex Reynolds
35k • written 15 days ago by
natami
▴ 10
2
votes
3
replies
303
views
Using GPUs in snakemake
Parabricks
gpu
snakemake
slurm
19 days ago by
raphael.B
▴ 520
1,000 results • Page
6 of 20
Recent Votes
High Malat-1 expression in single cell data
Segmentation fault using gemma
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
A: Insert Size And Fragment Size ?
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
which tool/software/package should I use to preprocess the rosetta-merck microarray platform raw data?
Recent Locations •
All
Turkey,
just now
United States,
just now
Spain,
just now
Germany,
1 minute ago
Israel,
1 minute ago
University Park, USA,
2 minutes ago
Germany,
3 minutes ago
Recent Awards •
All
Popular Question
to
SaltedPork
▴ 170
Popular Question
to
christopher medway
▴ 450
Popular Question
to
Mohita
▴ 50
Popular Question
to
Zhenyu Zhang
★ 1.2k
Popular Question
to
WUSCHEL
▴ 750
Teacher
to
Mensur Dlakic
★ 27k
Teacher
to
Jeremy Leipzig
22k
Recent Replies
Comment: Segmentation fault using gemma
by
dimpleadiwal050896
• 0
Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you
Comment: Can I merge Hi-C fastq files from different lanes?
by
GenoMax
141k
If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
Comment: What should I consider as FASTA for dataset?
by
GenoMax
141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository?
by
GenoMax
141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2
by
GenoMax
141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
Answer: High Malat-1 expression in single cell data
by
ATpoint
82k
My comment is general since I've never looked at this gene specifically, but metrics of poor cell quality in my experience never come alone…
Comment: What does it mean single base resolution in sequencing?
by
GenoMax
141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous
by
trausch
★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
Thats very intersting! What are the features in your classifier?
Comment: Limma Analysis Agilent Microarray Data (GPL1708)
by
hagl
▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
Lluís R.
★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better?
by
ATpoint
82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file
by
jkbonfield
★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I followed your advice and it seems that I'm getting results comparable to what I was getting before. Upon checking with `wc -l` on the ori…
Traffic: 2554 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