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 month
all time
today
this week
this month
this year
402 results • Page
1 of 9
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
13
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
41 minutes ago by
Alexandra
• 0
0
votes
0
replies
12
views
ReactomeGSA
ReactomeGSA
52 minutes ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
29
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 hours ago by
njornet
▴ 20
0
votes
0
replies
27
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmap
bbmerge
2 hours ago by
chrisk
• 0
0
votes
0
replies
50
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 6 hours ago by
GenoMax
142k • written 7 hours ago by
Dude
• 0
0
votes
0
replies
46
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
7 hours ago by
brunofelicianodeomena
• 0
0
votes
1
reply
90
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
4 hours ago by
sansan_96
▴ 90
0
votes
1
reply
125
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 13 hours ago by
GenoMax
142k • written 14 hours ago by
bioinfo
▴ 150
0
votes
2
replies
116
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
1 hour ago by
melissa.joubert
• 0
0
votes
0
replies
77
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
16 hours ago by
ramiro.barrantes
• 0
0
votes
0
replies
82
views
Is there a real ground truth for CNV data?
CNV
19 hours ago by
jennyp0706
• 0
1
vote
1
reply
110
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 14 hours ago by
Ram
43k • written 19 hours ago by
kilcdincer
▴ 10
0
votes
0
replies
70
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 20 hours ago by
GenoMax
142k • written 20 hours ago by
Bhavya
• 0
0
votes
3
replies
172
views
How to access GWAVA software of data
GWAVA
updated 20 hours ago by
GenoMax
142k • written 23 hours ago by
nonaddldy
▴ 10
0
votes
0
replies
78
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
153
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
318
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
144
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
144
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
135
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
98
views
reference-free assembly error assessment tools
assembly
1 day ago by
lagartija
▴ 160
0
votes
4
replies
231
views
Galaxy StringTie error
stringtie
galaxy
22 hours ago by
trkfs
• 0
0
votes
0
replies
97
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
1 day ago by
atariw
▴ 10
1
vote
4
replies
320
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 7 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
0
votes
1
reply
148
views
consensus sequence calling
consensus
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Ghada
• 0
0
votes
0
replies
84
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
1 day ago by
JACKY
▴ 140
0
votes
0
replies
96
views
Reference panel of normals for ensembl named refgenome
Mutect2
1 day ago by
gernophil
▴ 80
1
vote
0
replies
90
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
1 day ago by
tomas4482
▴ 400
3
votes
2
replies
177
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
101
views
lncRNA
tcga
lncrna
2 days ago by
jain72744
▴ 10
1
vote
2
replies
345
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
196
views
Output file of samtools flagstat empty
samtools-flagstat
updated 2 days ago by
colindaven
6.4k • written 2 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
2 days ago by
BioinfGuru
★ 1.7k
0
votes
4
replies
374
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
195
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
271
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 4 days ago by
Omics data mining
▴ 260
0
votes
5
replies
303
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
1 day 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 4 days ago by
GenoMax
142k • written 4 days ago by
maria.soler
• 0
0
votes
2
replies
280
views
How are score_weights calculated in this code?
single-cell
3 days ago by
carolofharvest
▴ 40
0
votes
1
reply
215
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
152
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
186
views
Microbial Signal Transduction Database
MiST
updated 5 days ago by
zx8754
11k • written 5 days ago by
Shravani
• 0
0
votes
0
replies
138
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
208
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
221
views
LncRNA Nomenclature
ENST
nomenclature
lncrna
GBB
ENSG
5 days ago by
jain72744
▴ 10
3
votes
1
reply
200
views
Question about methylation location
Methylation
WGBS
bisulfide
updated 4 days ago by
dthorbur
★ 2.0k • written 5 days ago by
Eren
• 0
0
votes
0
replies
150
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
164
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
402 results • Page
1 of 9
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Recent Locations •
All
South Korea,
1 minute ago
Milan, Italy,
2 minutes ago
Budapest,
3 minutes ago
Egypt,
4 minutes ago
UCLA,
5 minutes ago
Spain,
5 minutes ago
Hong Kong,
7 minutes ago
Recent Awards •
All
Popular Question
to
matteo.levorato
• 0
Popular Question
to
Palgrave
▴ 110
Popular Question
to
DBScan
▴ 300
Popular Question
to
chrisk
• 0
Popular Question
to
mbrav005
• 0
Popular Question
to
Sofia
• 0
Popular Question
to
jen
▴ 10
Recent Replies
Comment: RNA seq analysis
by
prifa
▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
by
dariober
14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype
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: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data
by
melissa.joubert
• 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Traffic: 2441 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