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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
15
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
41 minutes ago by
Lélé
• 0
0
votes
1
reply
50
views
genome finishing
finishing
genome
updated 43 minutes ago by
Joe
21k • written 3 hours ago by
trezini
• 0
0
votes
3
replies
83
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 hours ago by
Esraa
• 0
0
votes
1
reply
75
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
egascon
• 0
0
votes
0
replies
45
views
ReactomeGSA
ReactomeGSA
6 hours ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
67
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 hours ago by
GenoMax
142k • written 8 hours ago by
chrisk
• 0
0
votes
1
reply
68
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 46 minutes ago by
Joe
21k • written 10 hours ago by
iqra
• 0
0
votes
0
replies
58
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
Dude
• 0
0
votes
0
replies
54
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
12 hours ago by
brunofelicianodeomena
• 0
0
votes
1
reply
105
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
10 hours ago by
sansan_96
▴ 90
0
votes
1
reply
133
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 19 hours ago by
GenoMax
142k • written 19 hours ago by
bioinfo
▴ 150
0
votes
2
replies
144
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 hours ago by
melissa.joubert
• 0
0
votes
0
replies
87
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
22 hours ago by
ramiro.barrantes
• 0
0
votes
0
replies
87
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
1
vote
1
reply
121
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 20 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
0
replies
78
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Bhavya
• 0
0
votes
3
replies
183
views
How to access GWAVA software of data
GWAVA
updated 1 day ago by
GenoMax
142k • written 1 day ago by
nonaddldy
▴ 10
0
votes
0
replies
85
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
2
replies
165
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 day ago by
IdaHao0921
• 0
0
votes
3
replies
326
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
153
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
150
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 1 day ago by
GenoMax
142k • written 1 day ago by
cedric.blais
• 0
0
votes
1
reply
140
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 1 day ago by
Ram
43k • written 1 day ago by
eking28
• 0
0
votes
0
replies
100
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
0
votes
4
replies
237
views
Galaxy StringTie error
stringtie
galaxy
1 day ago by
trkfs
• 0
0
votes
0
replies
98
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
1
vote
4
replies
326
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 12 hours ago by
Juke34
8.6k • written 2 days ago by
Vijith
▴ 30
0
votes
1
reply
152
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 2 days ago by
Ghada
• 0
0
votes
0
replies
85
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
2 days ago by
JACKY
▴ 140
0
votes
0
replies
96
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
1
vote
0
replies
91
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
3
votes
2
replies
179
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 2 days ago by
ATpoint
82k • written 2 days ago by
jennyp0706
• 0
0
votes
0
replies
102
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
1
vote
2
replies
346
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 1 day ago by
Ram
43k • written 2 days ago by
t.fortunato.asquini
• 0
0
votes
2
replies
199
views
Output file of samtools flagstat empty
samtools-flagstat
updated 2 days ago by
colindaven
6.4k • written 3 days ago by
ramendra.sarma
• 0
0
votes
0
replies
104
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
3 days ago by
BioinfGuru
★ 1.7k
0
votes
4
replies
376
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
2 days ago by
beginner123
• 0
0
votes
2
replies
222
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
2 days ago by
analyst
▴ 50
0
votes
1
reply
197
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 4 days ago by
Ram
43k • written 4 days ago by
Shwetha
• 0
0
votes
0
replies
159
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 4 days ago by
naomiboldon
• 0
1
vote
3
replies
273
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 4 days ago by
Ram
43k • written 5 days ago by
Omics data mining
▴ 260
0
votes
5
replies
307
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 days ago by
SilhouetteQ
• 0
0
votes
1
reply
182
views
Alignment of samples with spike-in
alignment
multimapping
RNA-seq
ChIP-seq
spike-in
updated 5 days ago by
GenoMax
142k • written 5 days ago by
maria.soler
• 0
0
votes
2
replies
281
views
How are score_weights calculated in this code?
single-cell
4 days ago by
carolofharvest
▴ 40
0
votes
1
reply
217
views
How to convert Haps file to vcf file?
pre-phasing
GWAS
imputation
updated 4 days ago by
curious
▴ 750 • written 5 days ago by
SeoGyun
• 0
0
votes
0
replies
153
views
Trouble converting tfam and tped to map and ped files
plink
ped
tfam
tped
map
5 days ago by
Samantha
• 0
0
votes
1
reply
188
views
Microbial Signal Transduction Database
MiST
updated 5 days ago by
zx8754
11k • written 5 days ago by
Shravani
• 0
0
votes
0
replies
141
views
Allele specific expression of imprinted gens from 10x scRNA-seq data
scrna-seq
imprinted
10x
genes
5 days ago by
singcell
• 0
0
votes
1
reply
211
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Amr
▴ 160
0
votes
2
replies
224
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
5 days ago by
jain72744
▴ 10
1,000 results • Page
1 of 20
Recent Votes
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
Answer: Add samples IDs to Seurat object when integrating different samples to do differ
A: RNA-Seq analysis with Python
Answer: Add samples IDs to Seurat object when integrating different samples to do differ
Add samples IDs to Seurat object when integrating different samples to do differential expression analysis
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
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▴ 50
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Joe
21k
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yura.grabovska
▴ 70
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Recent Replies
Answer: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Papyrus
★ 2.9k
If you want to plot global accessibility, maybe you would like to plot the ATAC "signal", instead of specific peaks. In a very general mann…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
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: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> I haven't been able to figure out how to generate this plot. show us what you tried and the error messages
Comment: Duplicated reads (IDs) from nanopore sequencing
by
njornet
▴ 20
I think this is the answer but I can't find in the tags info about primary and secondary alignments. I've only found in the flag that the s…
Answer: Add stats to boxplot in R
by
Lélé
• 0
Hi, Have you tried switching the order of the stat_compare_means for the Wilcox with the one for kruskall-Wallis ?
Comment: genome finishing
by
Joe
21k
I may be wrong here so someone feel free to correct me, but I've never noticed a variants file from `SPAdes`, and certainly never used one …
Comment: perseus software (version 1.5.5)
by
Joe
21k
You will need to obtain the software from an official source. I believe Perseus is a paid-for program and as such sharing via the forum wou…
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
Joe
21k
This post does not fit the theme of this forum.
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
Istvan Albert
100k
this is not bioinformatics and is not a tool and as such it is off-topic on this site
Comment: calculating genomic coverage/ base overlap in R
by
Sayantani
• 0
# Install and load necessary packages if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") …
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
GenoMax
142k
Instead of simply posting a chunk of code it would be useful to add a line or two to say where this could would be useful. Not immediately …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
Thanks for the link. We never use "pod5_fail" folders when re-basecalling so we did not see this issue. Current version of MinKNOW now make…
Answer: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
with `findOverlaps` function in `GenomicRanges` package or directly with this package `GeneOverlap`. Check out the documentation of these …
Comment: Annotating file using bcftools
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…
Answer: Annotating file using bcftools
by
Pierre Lindenbaum
161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
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