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178 results • Page
1 of 4
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0
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0
replies
4
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Can I count UMI-barcode combination without mapping?
count
HyDrop
UMI
protein
UMI-Tools
1 minute ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
7
views
Can I count UMI-barcode combination without mapping?
count
HyDrop
UMI
protein
UMI-Tools
15 minutes ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
35
views
How do I check if a DNA sequence of a gene is supported by RNAseq data?
Genetics
RNA-seq
Phase-variation
Alignment
12 minutes ago by
Jack
• 0
0
votes
4
replies
634
views
Illumina EPIC v2 IlmnIDs and probe names
Illumina
EPIC
EPICv2
updated 1 hour ago by
Papyrus
★ 2.9k • written 6 months ago by
christine.a.pedersen
▴ 10
0
votes
3
replies
68
views
Best practices in Fungal Genome Assembly
illumina
assembly
nanopore
genome
updated 20 minutes ago by
samuel.a.odonnell
▴ 520 • written 3 hours ago by
Umer
▴ 50
0
votes
1
reply
70
views
Confirmation required on how DiffBind generates union of regions (min. 1bp overlap or gap)?
DiffBind
updated 2 hours ago by
GenoMax
142k • written 5 hours ago by
Ian
6.0k
1
vote
1
reply
95
views
Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
updated 3 hours ago by
ATpoint
82k • written 6 hours ago by
ev97
▴ 20
1
vote
8
replies
254
views
Error with pheatmap - 'from' must be a finite number
pheatmap
r
deseq2
updated 20 minutes ago by
SamGG
▴ 20 • written 17 hours ago by
vmpsb
• 0
0
votes
0
replies
45
views
Regarding ENSEMBL/Gencode and UCSC differences (ATAC-seq, ChiPseeker peaks annotation)
ATAC-seq
CHiPseeker
Annotation
6 hours ago by
Manko47
• 0
3
votes
7
replies
412
views
Z score
Z-score
updated 6 hours ago by
ATpoint
82k • written 5 days ago by
Akash D
▴ 60
1
vote
2
replies
123
views
Polygenic Risk Score calculation
snp
polygene
prs
variants
3 hours ago by
ashaneev07
▴ 20
2
votes
2
replies
324
views
Annotating single cell data automatically
single-cell
updated 8 hours ago by
Nat.Nataren
▴ 20 • written 5 weeks ago by
Gerard
• 0
0
votes
0
replies
48
views
EXOME DEPTH - CNV
CNV
9 hours ago by
Neha
• 0
0
votes
1
reply
77
views
coding and non-coding region of the viral genome
viral-genome
updated 55 minutes ago by
Ram
44k • written 9 hours ago by
Ghada
• 0
0
votes
2
replies
92
views
dbNSFP4.7a database format to Annovar Format?
snp
annovar
NGS
dbNSFP
updated 50 minutes ago by
Ram
44k • written 9 hours ago by
Clark_BioMorgan
▴ 50
0
votes
2
replies
134
views
Salmon ~ Effective Length
Salmon
updated 3 hours ago by
GenoMax
142k • written 13 hours ago by
chrisk
• 0
2
votes
3
replies
203
views
Search within posts based on tags using the Biostars API
api
meta
updated 1 hour ago by
Ram
44k • written 1 day ago by
Bálint
▴ 10
0
votes
0
replies
56
views
Funcotator gnomAD incoherent number of output fields
gatk
gnomAD
Funcotator
updated 47 minutes ago by
Ram
44k • written 13 hours ago by
jaime alvarez
▴ 30
0
votes
1
reply
115
views
Help with proteomics downstream analysis
mass-spectrometry
proteomics
updated 13 hours ago by
Ram
44k • written 23 hours ago by
Álvaro
• 0
0
votes
0
replies
55
views
How to Convert CNV Data to CNA Format for Reproducing Results with the Padma Package?
multi-omics
CNV
R
updated 13 hours ago by
Ram
44k • written 14 hours ago by
Ngrin
• 0
0
votes
0
replies
56
views
Calculating F_IS, F_IT on ancient DNA
adna
17 hours ago by
devenvyas
▴ 740
0
votes
0
replies
57
views
The number of region with the motif sequence is different between HOMER outputs
findMotifsGenome
HOMER
annotatePeaks
17 hours ago by
Aki
▴ 20
3
votes
3
replies
846
views
Cut&Run and heatmap
MACS2
bowtie2
updated 43 minutes ago by
Ram
44k • written 13 months ago by
qudrat.nii
▴ 10
3
votes
12
replies
5.3k
views
7 follow
txt file to bigwig
MEME
bigwig
updated 20 minutes ago by
GenoMax
142k • written 8.6 years ago by
tanni93
▴ 50
2
votes
2
replies
193
views
Help me with Heatmap
RNA-seq
R
DESeq2
updated 6 hours ago by
zx8754
11k • written 1 day ago by
vmpsb
• 0
0
votes
2
replies
123
views
identify the coordinate for coding and non_coding region.
coding
non_coding
22 hours ago by
Ghada
• 0
64
votes
25
replies
57k
views
22 follow
Download All The Bacterial Genomes From Ncbi
ncbi
updated 22 hours ago by
GenoMax
142k • written 11.4 years ago by
rehma.ar
▴ 290
3
votes
2
replies
144
views
How do i calculate the mean of triplicates in a data.frame based on pattern?
tidyverse
r
updated 6 hours ago by
zx8754
11k • written 1 day ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
178
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
8 hours ago by
Mohamed Abderrahmane
▴ 20
0
votes
0
replies
103
views
virus genome annotation
annotation
gff3
consensus
NCBI
coding_regions
22 hours ago by
Ghada
• 0
2
votes
6
replies
2.3k
views
Tool:
Python script to query GeneCards to get EntrezID, symbol from Ensembl geneID
biomart
annotation
Ensembl
updated 1 day ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
Shred
★ 1.4k
0
votes
0
replies
96
views
Subset of Transcripts- How do I proceed with it?
Stringite
Quantification
1 day ago by
Varsha
• 0
1
vote
2
replies
3.8k
views
How can run cd-hit-est with a clstr threshold less than 0.8?
cd-hit
cluster
updated 1 day ago by
Asaf
10k • written 6.3 years ago by
m.koohi.m
▴ 120
0
votes
2
replies
242
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 1 day ago by
a.alnawfal.1992
▴ 260 • written 5 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
80
views
PyRMD
Virtual
Screening
learning
cheminformatics
machine
1 day ago by
s
• 0
3
votes
4
replies
222
views
Invalid CIGAR after using bam clipOverlap
validatesamfile
cigar
bam
clipoverlap
1 day ago by
MboiTui
▴ 20
0
votes
0
replies
101
views
Determining rs ids from SNP HGV base ID?
rsID
HGV
SNP
updated 13 hours ago by
Ram
44k • written 1 day ago by
Katherine
• 0
0
votes
4
replies
281
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
Pseudobulk
single-cell
DESeq2
scRNA
updated 50 minutes ago by
jared.andrews07
★ 17k • written 2 days ago by
Sara
▴ 30
0
votes
1
reply
177
views
Facing problem with single cell rna seq annotation using singleR
annotation
singleR
scRNAseq
updated 1 day ago by
jared.andrews07
★ 17k • written 2 days ago by
sc_analysis
• 0
0
votes
0
replies
89
views
Imputed data doesn't match directly genotyped APOE genotype
APOE
directgenotyping
imputation
1 day ago by
kl
▴ 10
0
votes
0
replies
103
views
Tubemap multiseq
vg
1 day ago by
karciharun42
• 0
5
votes
3
replies
5.9k
views
Attempt to set 'rownames' on an object with no dimensions
R
microbiome
spieceasi
updated 1 day ago by
GenoMax
142k • written 3.6 years ago by
ks.sholohova
▴ 30
0
votes
0
replies
117
views
News:
Online course: Population Genomic Inference from Low-Coverage Whole-Genome Sequencing Data
Genotype-Likelihoods
Low-Coverage
Population-Genomics
ANGSD
updated 13 hours ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
226
views
How to decrease the motif score?
scores
Motif
updated 6 hours ago by
dthorbur
★ 2.0k • written 3 days ago by
Hadia
• 0
0
votes
0
replies
141
views
immuCell Abundance infiltrate
ImmuCell
Abundance
infiltrate
updated 3 days ago by
Pierre Lindenbaum
162k • written 3 days ago by
elbakri.fatimazahrae
• 0
1
vote
2
replies
244
views
Setting a threshold on gene expression for subsetting (scRNA-seq)
scRNA-seq
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
carolofharvest
▴ 40
0
votes
0
replies
139
views
MaxEntScan for rMATS results
MaxEntScan
rMATS
3 days ago by
adi.gershon1
• 0
0
votes
0
replies
444
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker.
MAKER.
annotation.
3 days ago by
Sony
▴ 10
0
votes
0
replies
151
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
3 days ago by
F110152169
• 0
4
votes
2
replies
251
views
Number of non-ATCG nucleotides replaced by Salmon
rna-seq
stringtie
salmon
updated 13 hours ago by
Ram
44k • written 3 days ago by
Tonya S.
▴ 10
178 results • Page
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Answer: UMI-Tools knee-method has great influence on the results of white list
Answer: UMI-Tools knee-method has great influence on the results of white list
linkage disequilibrium analysis
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
Answer: linkage disequilibrium analysis
Answer: UMI-Tools knee-method has great influence on the results of white list
A: Fix SAM flags on quality filtered paired-end BAM file
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Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
by
Jack
• 0
I have the DNA sequences of every phase variable locus in the genomes of 8 bacterial isolates. Repeats range from polyG tracts around 9-20…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 520
For the short-read strains: <br/> I would recommend just using SPADES For the strains with long-reads: <br/> I think spades and masurca as…
Comment: txt file to bigwig
by
GenoMax
142k
Click on `edit`. That should open the edit window which will have a `Delete` button at bottom right to delete the comment/reply.
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★ 1.9k
Can you pls make it an answer so that I can accept it? thx
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴ 520
I think tools like quickmerge (or Ragtag's patch command) can help for long-read assemblies, but I would definitely avoid using them with s…
Comment: txt file to bigwig
by
sogand
• 0
Hi, I tried to delete my comment but can't see any delete/remove option here! Thanks
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
You'd see a different issue if the vector being analyzed contained character entries. This is clearly a problem with NA/NaN/Inf values in t…
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
by
GenoMax
142k
> bacterial genes containing phase variable short sequence repeats in their coding regions Can you describe this in a bit more detail? Are…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2
by
jared.andrews07
★ 17k
This is exactly my point. You should not have gotten data to this state unintentionally, so you need to double-check what was done upstream…
Comment: Search within posts based on tags using the Biostars API
by
Ram
44k
Right, that's true. One way to do that would be to get the HTML output of https://www.biostars.org/tag/crispr/ and search it for the first …
Answer: Illumina EPIC v2 IlmnIDs and probe names
by
Papyrus
★ 2.9k
The ID code and the new features for the EPICv2 are explained in the Illumina documentation which you can access [here][1], in the `Infiniu…
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
That answers half of what I asked you. Where's the output to the first command?
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
You already have the response to the first one, so there was no need to include that.
Answer: Illumina EPIC v2 IlmnIDs and probe names
by
GenoMax
142k
The answer is provided in this Bioconductor thread: https://support.bioconductor.org/p/9156675/
Comment: Illumina EPIC v2 IlmnIDs and probe names
by
rna-seq_researcher
▴ 60
Hi, by any chance did you manage to solve this problem?
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