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11,719 results • Page
2 of 235
Sort: Rank
Rank
Views
Votes
Replies
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
0
votes
3
replies
383
views
Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
3 days ago by
Brian Bushnell
20k
2
votes
11
replies
790
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 2 days ago by
Ram
44k • written 11 days ago by
hannes.bongartz
• 0
0
votes
2
replies
241
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
1 day ago by
marco.barr
▴ 130
0
votes
0
replies
159
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
3 days ago by
niconps14
• 0
3
votes
5
replies
393
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 2 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
QX
• 0
2
votes
6
replies
432
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 1 day ago by
jared.andrews07
★ 17k • written 4 days ago by
Picasa
▴ 640
2
votes
1
reply
217
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 4 days ago by
Jeremy Leipzig
22k • written 4 days ago by
liaotsungjen
▴ 10
0
votes
0
replies
144
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 4 days ago by
Ram
44k • written 4 days ago by
Alessia
• 0
1
vote
3
replies
301
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 3 days ago by
Bastien Hervé
5.3k • written 4 days ago by
Sara
▴ 30
0
votes
1
reply
187
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 3 days ago by
Ram
44k • written 4 days ago by
garcesj
▴ 50
0
votes
1
reply
3.0k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 4 days ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
1
reply
402
views
LDhat lookup table
LDhat
updated 4 days ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
1
reply
205
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
updated 1 day ago by
raphael.B
▴ 520 • written 4 days ago by
irebekah.c
• 0
0
votes
0
replies
143
views
Can you use a polygenic risk score for a trait (e.g., BMI) in association analyses when it doesn't associate with BMI in the sample it is used?
polygenic-risk-score
imputation
updated 4 days ago by
Ram
44k • written 4 days ago by
kl
▴ 10
0
votes
5
replies
268
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
3 days ago by
Deepthi
• 0
1
vote
4
replies
329
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
3 days ago by
sc_analysis
• 0
0
votes
1
reply
209
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 4 days ago by
Bastien Hervé
5.3k • written 4 days ago by
bio_info
▴ 20
3
votes
4
replies
500
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 4 days ago by
fracarb8
★ 1.7k • written 11 days ago by
txema.heredia
▴ 130
0
votes
0
replies
167
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
4 days ago by
doramora
▴ 10
0
votes
1
reply
162
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
updated 5 hours ago by
dthorbur
★ 2.0k • written 4 days ago by
Emily
▴ 20
2
votes
3
replies
270
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
4 days ago by
hashim.rana11
▴ 20
0
votes
1
reply
188
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 4 days ago by
Pierre Lindenbaum
162k • written 4 days ago by
Maksim
• 0
1
vote
2
replies
285
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
4 days ago by
F110152169
• 0
8
votes
10
replies
3.2k
views
8 follow
Venter Genome Vcf
vcf
updated 19 hours ago by
Jeremy Leipzig
22k • written 10.1 years ago by
win
▴ 980
0
votes
0
replies
159
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 4 days ago by
Ram
44k • written 4 days ago by
Christopher
▴ 10
4
votes
1
reply
239
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
May Ling
• 0
0
votes
0
replies
135
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 4 days ago by
GenoMax
142k • written 4 days ago by
jway
• 0
0
votes
3
replies
398
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 4 days ago by
ATpoint
82k • written 4 days ago by
shahzaibali
• 0
0
votes
1
reply
198
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 4 days ago by
jared.andrews07
★ 17k • written 5 days ago by
atan
• 0
0
votes
2
replies
251
views
What do the transcript variant # mean in RefSeq?
refseq
updated 4 days ago by
Ram
44k • written 4 days ago by
curious
▴ 750
4
votes
6
replies
437
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
4 days ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
328
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 4 days ago by
Jeremy
▴ 910 • written 5 days ago by
Mohamed Samir
▴ 30
2
votes
0
replies
227
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
5 days ago by
Matthias Zepper
4.6k
0
votes
1
reply
173
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 5 days ago by
Ram
44k • written 5 days ago by
a.bibek52
▴ 10
3
votes
7
replies
4.0k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 5 days ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
203
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
4 days ago by
mtabaka
• 0
0
votes
1
reply
166
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 5 days ago by
Papyrus
★ 2.9k • written 5 days ago by
June
• 0
0
votes
2
replies
684
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 5 days ago by
June
• 0 • written 10 months ago by
rkb965
• 0
4
votes
6
replies
340
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
4 days ago by
bio_info
▴ 20
3
votes
3
replies
237
views
Unexpected read length from NGS
NGS
Illumina
4 days ago by
QX
• 0
1
vote
7
replies
403
views
samtools write-index
samtools
1 day ago by
R.L.
• 0
2
votes
3
replies
316
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
1 day ago by
Varsha
• 0
3
votes
2
replies
183
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 5 days ago by
ATpoint
82k • written 5 days ago by
egascon
• 0
0
votes
0
replies
92
views
GWAS or QTL mapping in RIL population
GWAS
RIL
5 days ago by
韩雨
• 0
0
votes
0
replies
96
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 5 days ago by
Ram
44k • written 5 days ago by
emmanouil.a
▴ 120
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 5 days ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
272
views
GWAS Phenotypes
GWAS
updated 5 days ago by
韩雨
• 0 • written 6 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.2k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 5 days ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
1
vote
1
reply
139
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 5 days ago by
GenoMax
142k • written 5 days ago by
azeu
▴ 10
11,719 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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