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 week
all time
today
this week
this month
this year
108 results • Page
1 of 3
Sort: replies
Rank
Views
Votes
Replies
0
votes
10
replies
375
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
2
votes
9
replies
804
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
8
replies
283
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 8 days ago by
quentinperriere
• 0
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
1
vote
5
replies
245
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
0
votes
5
replies
201
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 21 hours ago by
GenoMax
141k • written 21 hours ago by
Bertalan_Takacs
▴ 90
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 5 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
2
votes
5
replies
429
views
Marking duplicates using UMIs
Deduplication
UMI
updated 3 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
2
votes
5
replies
676
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
0
votes
5
replies
275
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
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 6 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
4
replies
572
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
6 days ago by
Kai Xin
• 0
2
votes
4
replies
243
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
1 day ago by
samuelkalandarov2002
▴ 10
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
4
replies
192
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
3 hours ago by
sehriban.buyukkilic
▴ 10
3
votes
3
replies
463
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
1
vote
3
replies
193
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 6 days ago by
Ram
43k • written 9.0 years ago by
siddharth.patel.153
• 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
3
replies
229
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
0
votes
2
replies
417
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
0
votes
2
replies
180
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 days ago by
Ashok
• 0
0
votes
2
replies
257
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
0
votes
2
replies
372
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
6 days ago by
Ashok
• 0
0
votes
2
replies
532
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS
exome-sequencing
batch-effect
updated 6 days ago by
Ram
43k • written 6.5 years ago by
Alternative
▴ 270
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma
RNA-Seq
edgeR
batch-effect
updated 6 days ago by
Ram
43k • written 7.0 years ago by
endikavarela
• 0
0
votes
2
replies
537
views
autodockvina
python
python3
autodock
updated 6 days ago by
Ram
43k • written 4 months ago by
iamsmor
• 0
0
votes
2
replies
87
views
Highest variable features in single cell data
cell
single
1 hour ago by
Kazo
• 0
1
vote
2
replies
226
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 17 days ago by
Netanel
• 0
0
votes
2
replies
215
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 16 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
1
vote
2
replies
158
views
alignment result
RNA-seq
samtools
hisat2
5 hours ago by
ahmad.sajad4541
• 0
0
votes
1
reply
818
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 6 days ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
0
votes
1
reply
279
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
0
votes
1
reply
126
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 6.6 years ago by
boymin2020
▴ 80
0
votes
1
reply
109
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 20 hours ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
1
reply
122
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 2 days ago by
Susmita Mandal
▴ 110
0
votes
1
reply
142
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
0
votes
1
reply
144
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
1
vote
1
reply
157
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 2 days ago by
Kasturi
• 0
1
vote
1
reply
412
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 6 days ago by
Chris
▴ 260
0
votes
1
reply
134
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 2 days ago by
Cameron.walker9900
• 0
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
1
vote
1
reply
389
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 days ago by
renan.igor
• 0
0
votes
1
reply
115
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
108 results • Page
1 of 3
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
Recent Locations •
All
United States,
just now
Bologna,
2 minutes ago
Netherlands,
3 minutes ago
Russia,
3 minutes ago
France,
3 minutes ago
United Kingdom,
4 minutes ago
Finland,
6 minutes ago
Recent Awards •
All
Popular Question
to
Hamtaro
▴ 50
Popular Question
to
Nicolas Rosewick
11k
Popular Question
to
Assa Yeroslaviz
★ 1.8k
Popular Question
to
Keem Uarren Eiryll
• 0
Centurion
to
analyst
▴ 30
Popular Question
to
anasjamshed
▴ 120
Popular Question
to
camillab.
▴ 160
Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Traffic: 2543 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