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1,000 results • Page
1 of 20
Sort: Rank
Rank
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Votes
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0
votes
0
replies
15
views
scRNA data analysis , how to compare pattern in multiple samples
R
Bioinformatics
scRNA
data
1 hour ago by
Confused_human
▴ 20
0
votes
0
replies
32
views
Tool:
retroSeeker: discovering novel retrotransposons in humans and any species
element
Expression
Evolution
Retrotransposon
Mobile
3 hours ago by
lsp03yjh
▴ 850
0
votes
0
replies
40
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
5 hours ago by
qiuting
• 0
0
votes
0
replies
42
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
6 hours ago by
Agnia
• 0
1
vote
4
replies
182
views
Where can I get a list of SNPs mapping overlapping genes in humans?
SNPs
updated 9 hours ago by
Alex Reynolds
35k • written 10 hours ago by
Mr Locuace
▴ 150
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
1
reply
107
views
How to add exon annotations to genome annotation
proteome
genome
BED
annotation
updated 10 hours ago by
alex.zaccaron
▴ 380 • written 10 hours ago by
Simone
▴ 10
0
votes
0
replies
62
views
News:
University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023
expression
singlecell
rnaseq
11 hours ago by
mia.nahom
▴ 10
2
votes
3
replies
149
views
Annotation Visualization IGV
igv
alignment
gff
annotation
visualization
updated 11 hours ago by
Pierre Lindenbaum
158k • written 11 hours ago by
awhale01
• 0
0
votes
6
replies
276
views
Resolving over clustered NGS with Q-scores
NGS
phred
Q-score
overclustering
9 hours ago by
sam.himes92
• 0
4
votes
2
replies
213
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
11 hours ago by
EK
• 0
0
votes
1
reply
112
views
Curated model organism gene functional annotations
Interpro
C.elegans
GO-terms
updated 15 hours ago by
Ram
41k • written 16 hours ago by
ian.will
▴ 10
2
votes
4
replies
298
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
16 hours ago by
cucindarko51
• 0
1
vote
10
replies
1.8k
views
Scanpy Pearson residual PCA error
python
scRNA
scanpy
PCA
updated 17 hours ago by
Maëlick
• 0 • written 15 months ago by
Emily
▴ 70
0
votes
0
replies
67
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
17 hours ago by
Ming Tommy Tang
★ 3.6k
0
votes
2
replies
148
views
Very low successfully assigned alignments with feature counts
featureCounts
RNA-seq
updated 15 hours ago by
Istvan Albert
99k • written 17 hours ago by
Manuel
• 0
0
votes
4
replies
245
views
Need help to find FASTA sequence from dbSNP
dbSNP
SNP
FASTA
updated 17 hours ago by
GenoMax
136k • written 23 hours ago by
syedahumairagillani
• 0
5
votes
5
replies
325
views
Calculate GC content for entire chromosome
bam
GC
assembly
bwa-mem
updated 16 hours ago by
colindaven
5.8k • written 1 day ago by
skilleta0527
• 0
4
votes
2
replies
170
views
Execute R command on specific termimal
R
updated 15 hours ago by
Ram
41k • written 21 hours ago by
QX
• 0
1
vote
1
reply
168
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
updated 15 hours ago by
Ram
41k • written 1 day ago by
O.rka
▴ 710
0
votes
0
replies
71
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
1 day ago by
junhuili
• 0
1
vote
5
replies
830
views
Strandedness of RNA-seq results
dual-RNA-seq
featurecounts
strandedness
HISAT2
updated 1 day ago by
charles.feigin
• 0 • written 18 months ago by
jamesymtang
▴ 10
1
vote
1
reply
1.0k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 1 day ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
77
views
megablast taxonomy assign in blobtools
blobtools
1 day ago by
bs
• 0
0
votes
1
reply
140
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
updated 15 hours ago by
5heikki
11k • written 1 day ago by
George X.
• 0
0
votes
1
reply
141
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 15 hours ago by
Ram
41k • written 1 day ago by
Shloka
• 0
0
votes
1
reply
141
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
1 day ago by
LauferVA
3.8k
4
votes
15
replies
6.4k
views
8 follow
bbmap split paired-end reads back into separated fastq files?
genome
next-gen-sequencing
bbmap
alignment
updated 1 day ago by
GenoMax
136k • written 5.2 years ago by
c.e.chong
▴ 60
0
votes
1
reply
151
views
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException
phg
updated 1 day ago by
lcj34
▴ 250 • written 1 day ago by
ryan
• 0
1
vote
1
reply
135
views
ANNOVAR Download Failing
ANNOVAR
updated 1 day ago by
Ram
41k • written 1 day ago by
tony
• 0
0
votes
1
reply
144
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 1 day ago by
Ram
41k • written 1 day ago by
mgranada3
▴ 30
0
votes
2
replies
198
views
Downsampling ATAC-seq BAM files
ATAC-seq
1 day ago by
Elise
• 0
0
votes
0
replies
86
views
spatial metabolomics, python
spatial-metabolomics
updated 1 day ago by
Ram
41k • written 1 day ago by
joha
▴ 10
0
votes
3
replies
331
views
RNA seq
Differential-gene-expression
updated 1 day ago by
jv
★ 1.3k • written 3 days ago by
Byonkesh
• 0
0
votes
4
replies
440
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
updated 1 day ago by
Ram
41k • written 5 days ago by
fluke
• 0
1
vote
4
replies
211
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Javier
• 0
0
votes
0
replies
101
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
1 day ago by
kdca
• 0
0
votes
2
replies
192
views
Issues while running blastx
blastx
RNA-seq
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Foad
▴ 10
0
votes
1
reply
134
views
Tophat2 Error running 'long_spanning_reads' on M1 Mac
Tophat2
Boost
RiboSeq
M1-Mac
updated 1 day ago by
Ram
41k • written 1 day ago by
riboseq938
• 0
0
votes
1
reply
165
views
Contrasts in R
contrasts
r
updated 1 day ago by
jv
★ 1.3k • written 1 day ago by
SGMS
▴ 130
1
vote
5
replies
645
views
ATAC-Seq and RPKM
RPKM
ATAC-Seq
updated 1 day ago by
ATpoint
78k • written 9 weeks ago by
qudrat.nii
• 0
0
votes
1
reply
1.3k
views
Correlation RNA-seq and ATAC-seq
RNA-Seq
R
gene
updated 1 day ago by
Tao Zhu
▴ 10 • written 3.4 years ago by
pastel950818
• 0
5
votes
4
replies
881
views
Methods to integrate ATAC-seq and RNA-seq
RNA-seq
ATAC-seq
updated 1 day ago by
Tao Zhu
▴ 10 • written 4 months ago by
Chris
▴ 230
0
votes
1
reply
140
views
Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release
bcftools
dbSNP
tabix
vcf
updated 1 day ago by
Ram
41k • written 1 day ago by
Fernando
• 0
0
votes
1
reply
444
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 1 day ago by
Joe
21k • written 1 day ago by
Ralph
• 0
1
vote
2
replies
184
views
contrast file in DESeq2 bioconductor
DEseq2
updated 1 day ago by
Ram
41k • written 1 day ago by
r.shiasi3897
▴ 10
1
vote
2
replies
311
views
Best method for batch correction of three datasets
RNA-seq
updated 23 hours ago by
ATpoint
78k • written 1 day ago by
CTLong
▴ 20
0
votes
1
reply
151
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 1 day ago by
Ram
41k • written 1 day ago by
francesco.degiglio
• 0
0
votes
0
replies
108
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
1 day ago by
sil_bioinfo
▴ 40
0
votes
0
replies
99
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
1 day ago by
Saad Khan
▴ 420
1,000 results • Page
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Recent Votes
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
Answer: Calculate GC content for entire chromosome
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
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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. :)
Comment: Resolving over clustered NGS with Q-scores
by
Trivas
★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores
by
Trivas
★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores
by
sam.himes92
• 0
Yes at 5%.
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