Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : this week
all time
today
this week
this month
this year
89 results • Page
2 of 2
Sort: replies
Rank
Views
Votes
Replies
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
1
vote
1
reply
447
views
ComBat_Seq stuck adjusting the data
Batch-Effect
RNAseq
ComBat-Seq
updated 6 days ago by
Jaïr
• 0 • written 4 months ago by
NorbertK
▴ 10
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
92
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 4 hours ago by
Joe
21k • written 13 hours ago by
iqra
• 0
1
vote
0
replies
138
views
What is Deepvariant default filtering values ?
vcf
calling
filter
variant
deepvariant
6 days ago by
Shae
▴ 10
0
votes
0
replies
179
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
6 days ago by
Winter
• 0
0
votes
0
replies
82
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
0
replies
92
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
0
votes
0
replies
92
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
1 day ago by
ramiro.barrantes
• 0
0
votes
0
replies
61
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
16 hours ago by
brunofelicianodeomena
• 0
0
votes
0
replies
65
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
Dude
• 0
0
votes
0
replies
107
views
Pathway analysis of Bacteria from denovo genome assembly
KEGG-KASS
WGS
Pathway
denovo
updated 6 days ago by
Ram
43k • written 7 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
50
views
ReactomeGSA
ReactomeGSA
9 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
116
views
Summary Statistics SNPs not found in Target data
SNP
plink
PRS
updated 6 days ago by
Ram
43k • written 6 days ago by
curious_butterfly
• 0
0
votes
0
replies
121
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep
vcf
gnomad
6 days ago by
asalimih
▴ 60
0
votes
0
replies
167
views
How do I calculate SE or P value if I only have BETA
prscsx
beta
se
pvalue
updated 5 days ago by
zx8754
11k • written 5 days ago by
curious_butterfly
• 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
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
0
replies
89
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
0
replies
160
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 4 days ago by
Ram
43k • written 5 days ago by
naomiboldon
• 0
0
votes
0
replies
152
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification
Metagenomics
Krona
Kraken2
5 days ago by
Aytaç
• 0
0
votes
0
replies
157
views
supervised admixture
supervised
admixture
5 days ago by
RT
▴ 10
0
votes
0
replies
38
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
4 hours ago by
Lélé
• 0
0
votes
0
replies
105
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
0
replies
47
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 3 hours ago by
ATpoint
82k • written 4 hours ago by
yura.grabovska
▴ 70
0
votes
0
replies
104
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
0
votes
0
replies
29
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
2 hours ago by
jway
• 0
0
votes
0
replies
20
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
1 hour ago by
diqixiaoyaoer
▴ 10
1
vote
0
replies
91
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
2 days ago by
tomas4482
▴ 400
0
votes
0
replies
97
views
Reference panel of normals for ensembl named refgenome
Mutect2
2 days ago by
gernophil
▴ 80
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
186
views
What is workflow for de-novo assembling of nuclear and mito genomes of non-model organisms
de-novo
WGS
DNA-seq
assembling
6 days ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
99
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
2 days ago by
atariw
▴ 10
0
votes
0
replies
101
views
reference-free assembly error assessment tools
assembly
2 days ago by
lagartija
▴ 160
0
votes
0
replies
114
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass-spectrometry
Proteins
updated 1 day ago by
Ram
43k • written 16 days ago by
atharvakarkare14
▴ 30
1
vote
0
replies
176
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
6 days ago by
eebloom
▴ 80
0
votes
0
replies
180
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
1 day ago by
Emily
▴ 20
0
votes
0
replies
106
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
6 days ago by
Javier
• 0
0
votes
0
replies
10
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
25 minutes ago by
Rodolfo Adrián
• 0
89 results • Page
2 of 2
Recent Votes
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Recent Locations •
All
Canada,
1 minute ago
Memphis, TN,
1 minute ago
United States,
3 minutes ago
United States,
3 minutes ago
United States,
3 minutes ago
United States,
6 minutes ago
United States,
6 minutes ago
Recent Awards •
All
Scholar
to
rpolicastro
13k
Popular Question
to
Amr
▴ 160
Popular Question
to
asalimih
▴ 60
Popular Question
to
nd48
▴ 20
Scholar
to
Trivas
★ 1.8k
Popular Question
to
biology_inform
▴ 50
Popular Question
to
Joe
21k
Recent Replies
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Traffic: 2577 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6