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27 results • Page
1 of 1
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Views
Votes
Replies
5
votes
4
replies
6.0k
views
How is "integer score for display" calculated in MACS2
ChIP-Seq
MACS2
narrowPeak
updated 16 hours ago by
SplitInf
▴ 10 • written 7.2 years ago by
Vanilla
▴ 110
1
vote
10
replies
1.8k
views
Scanpy Pearson residual PCA error
python
scRNA
scanpy
PCA
updated 18 hours ago by
Maëlick
• 0 • written 15 months ago by
Emily
▴ 70
7
votes
17
replies
1.1k
views
Building reference dbSNP file using WGS samples
NGS
WGS
Variant-calling
non-model
Bootstrapping
22 hours ago by
analyst
▴ 10
0
votes
0
replies
693
views
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
SNV
mutationMatrix
tumorPhylogeny
scDNAseq
mutaion
13 hours ago by
supernovamik
• 0
2
votes
6
replies
499
views
6 follow
STAR ALIGNMENT
alignment-rate
updated 24 minutes ago by
Hải Đăng
• 0 • written 19 days ago by
Hanh
▴ 20
6
votes
5
replies
334
views
Calculate GC content for entire chromosome
bam
GC
assembly
bwa-mem
updated 18 hours ago by
colindaven
5.8k • written 1 day ago by
skilleta0527
• 0
2
votes
4
replies
304
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
18 hours ago by
cucindarko51
• 0
0
votes
6
replies
289
views
Resolving over clustered NGS with Q-scores
NGS
phred
Q-score
overclustering
11 hours ago by
sam.himes92
• 0
0
votes
4
replies
251
views
Need help to find FASTA sequence from dbSNP
dbSNP
SNP
FASTA
updated 19 hours ago by
GenoMax
136k • written 1 day ago by
syedahumairagillani
• 0
0
votes
1
reply
246
views
News:
RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
NGS
RNA-Seq
Workshop
1 hour ago by
David Langenberger
10k
1
vote
4
replies
244
views
vcftools
vcftools
2 hours ago by
sevda
• 0
4
votes
2
replies
219
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
13 hours ago by
EK
• 0
1
vote
4
replies
198
views
Where can I get a list of SNPs mapping overlapping genes in humans?
SNPs
updated 11 hours ago by
Alex Reynolds
35k • written 12 hours ago by
Mr Locuace
▴ 150
4
votes
2
replies
176
views
Execute R command on specific termimal
R
updated 17 hours ago by
Ram
41k • written 23 hours ago by
QX
• 0
1
vote
1
reply
173
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
updated 17 hours ago by
Ram
41k • written 1 day ago by
O.rka
▴ 710
2
votes
3
replies
159
views
Annotation Visualization IGV
igv
alignment
gff
annotation
visualization
updated 13 hours ago by
Pierre Lindenbaum
158k • written 13 hours ago by
awhale01
• 0
0
votes
2
replies
152
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 16 hours ago by
Istvan Albert
99k • written 19 hours ago by
Manuel
• 0
0
votes
1
reply
145
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
updated 17 hours ago by
5heikki
11k • written 1 day ago by
George X.
• 0
0
votes
1
reply
145
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 17 hours ago by
Ram
41k • written 1 day ago by
Shloka
• 0
0
votes
1
reply
116
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 17 hours ago by
Ram
41k • written 18 hours ago by
ian.will
▴ 10
0
votes
1
reply
114
views
How to add exon annotations to genome annotation
proteome
genome
BED
annotation
updated 12 hours ago by
alex.zaccaron
▴ 380 • written 12 hours ago by
Simone
▴ 10
1
vote
0
replies
74
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
19 hours ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
68
views
News:
University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023
expression
singlecell
rnaseq
13 hours ago by
mia.nahom
▴ 10
0
votes
1
reply
55
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
20 minutes ago by
qiuting
• 0
0
votes
1
reply
54
views
scRNA data analysis , how to compare pattern in multiple samples
R
Bioinformatics
scRNA
data
updated 1 hour ago by
ATpoint
78k • written 3 hours ago by
Confused_human
▴ 20
0
votes
0
replies
48
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
8 hours ago by
Agnia
• 0
0
votes
0
replies
44
views
Tool:
retroSeeker: discovering novel retrotransposons in humans and any species
element
Expression
Evolution
Retrotransposon
Mobile
5 hours ago by
lsp03yjh
▴ 850
27 results • Page
1 of 1
Recent Votes
Answer: Calculate GC content for entire chromosome
STAR ALIGNMENT
STAR ALIGNMENT
Best method for batch correction of three datasets
CITEseq tutorial
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
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5.8k
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3.5k
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jared.andrews07
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Comment: absolute running error: Error in if (!is.na(res)) { : the condition has length >
by
qiuting
• 0
this is the error.log: Detected error in sample P01_1 Error message: the condition has length > 1 Where: if !is.na(res) { mode.tab[(i…
Comment: STAR ALIGNMENT
by
Hải Đăng
• 0
Sis, where are you currently working? How can I get in touch with you?
Answer: RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
by
David Langenberger
10k
We already have an incredible number of registrations for this time. If you still want to be there, then you should register soon!
Comment: scRNA data analysis , how to compare pattern in multiple samples
by
ATpoint
78k
Can you please ask a precise question rather than posting a wall of code? What is the main problem you have, what did you try? Did you foll…
Comment: vcftools
by
sevda
• 0
Hello, Thank you for your attention. It ran successfully and I got no errors or warnings but no new files were created.
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Ram
41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
by
Alex Reynolds
35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation
by
alex.zaccaron
▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV
by
awhale01
• 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV
by
Pierre Lindenbaum
158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts
by
EK
• 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
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