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
181 results • Page
2 of 4
Sort: Votes
Rank
Views
Votes
Replies
1
vote
5
replies
800
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
written 6 months ago by
Daniel
▴ 30
1
vote
1
reply
100
views
constructing pangenome through psvcp
psvcp
pangenome
1 hour ago by
analyst
▴ 50
1
vote
3
replies
207
views
Genotyping sites with N in reference genome
GATK
UnifiedGenotyper
updated 2 days ago by
Zhenyu Zhang
★ 1.2k • written 2 days ago by
shpak.max
▴ 50
1
vote
4
replies
290
views
Add stats to boxplot in R
stats
R
2 days ago by
Ghada
• 0
1
vote
4
replies
295
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 4 hours ago by
Joe
21k • written 9 days ago by
cput
• 0
1
vote
5
replies
264
views
Annotating file using bcftools
annotation
plink
bcftools
2 days ago by
kl
▴ 10
1
vote
2
replies
224
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
2 days ago by
MarcosCosta
• 0
1
vote
1
reply
247
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 0
1
vote
1
reply
115
views
RNAseq coverage vs depth for transcript isoform expression?
RNAseq
updated 2 hours ago by
Gordon Smyth
★ 7.2k • written 17 hours ago by
marineandriot
• 0
1
vote
1
reply
174
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Pegasus
▴ 100
1
vote
1
reply
172
views
mitochondrial genome assembly pipeline
mammals
mitochondrial-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
m90
▴ 30
1
vote
4
replies
284
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
1
vote
2
replies
228
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
2 days ago by
bioinfo
▴ 150
1
vote
5
replies
302
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 22 hours ago by
dthorbur
★ 2.0k • written 1 day ago by
BATMAN
• 0
1
vote
1
reply
147
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 3 days ago by
Ram
43k • written 4 days ago by
kilcdincer
▴ 10
1
vote
3
replies
272
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
GenoMax
142k • written 4 days ago by
ohtang7
▴ 40
1
vote
8
replies
433
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
updated 12 hours ago by
Alex Reynolds
35k • written 4 days ago by
ntsopoul
▴ 60
1
vote
2
replies
363
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 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 0
1
vote
3
replies
799
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon
chromosome
polish
genome
draft
updated 1 day ago by
sansan_96
▴ 90 • written 2.7 years ago by
boymin2020
▴ 80
1
vote
1
reply
185
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Jordan M Eizenga
▴ 460 • written 12 days ago by
sarumonsus
▴ 10
1
vote
2
replies
210
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 3 days ago by
colindaven
6.4k • written 3 days ago by
mbrav005
• 0
1
vote
2
replies
183
views
Duplicated sequence samtools
bowtie2
samtools
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Moinuddin
• 0
1
vote
3
replies
437
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
4 days ago by
kalavattam
▴ 190
1
vote
0
replies
118
views
News:
Course on Manual Genome Curation
Genome-Assembly
Pretext-View
Manual-Genome-Curation
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
1
vote
5
replies
270
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq
deseq2
updated 1 day ago by
Ram
43k • written 2 days ago by
manuelmourato25
• 0
1
vote
1
reply
179
views
Tool:
Collect dispersed executable files and run them by using bingo.
bingo
updated 1 day ago by
Ram
43k • written 2 days ago by
dwpeng
▴ 10
1
vote
3
replies
258
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
offtopic
Degrees
python
updated 1 day ago by
Ram
43k • written 3 days ago by
kuttibiotech2009
▴ 30
1
vote
16
replies
687
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 1 hour ago by
GenoMax
142k • written 2 days ago by
hophuquy0944
• 0
1
vote
5
replies
218
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
updated 3 days ago by
Pierre Lindenbaum
161k • written 3 days ago by
biology_inform
▴ 50
1
vote
4
replies
342
views
Contig assembly task, errors
dna
genetics
contig
assembly
updated 4 days ago by
Ram
43k • written 9 days ago by
samRayne
• 0
1
vote
0
replies
98
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
5 days ago by
tomas4482
▴ 400
1
vote
1
reply
167
views
API kegg - IndexError: list index out of range
kegg
API
updated 1 day ago by
Nyksubuz
▴ 20 • written 2 days ago by
mirwa.zidi93
• 0
0
votes
7
replies
446
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 5 days ago by
Mohamed Abderrahmane
▴ 20 • written 19 days ago by
matteo.levorato
• 0
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by
beginner123
• 0
0
votes
3
replies
165
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 days ago by
Esraa
• 0
0
votes
1
reply
48
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 4 hours ago by
ATpoint
82k • written 4 hours ago by
Jacek
▴ 20
0
votes
9
replies
610
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 3 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
0
votes
0
replies
110
views
Is it okay to assemble my 12 metatranscriptome samples with Trinity separately?
trinity
metatranscriptome
3 days ago by
jway
• 0
0
votes
1
reply
140
views
Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
annotation
vcf
vep
zygosity
deepvariant
3 days ago by
asalimih
▴ 60
0
votes
5
replies
270
views
calculating genomic coverage/ base overlap in R
genomics
updated 3 hours ago by
1769mkc
★ 1.2k • written 3 days ago by
Xbox_27
• 0
0
votes
0
replies
113
views
DOCK6 installation on MacOS M1
installation
troubleshooting
DOCK6
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Rodolfo Adrián
• 0
0
votes
9
replies
602
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 days ago by
Arton
▴ 10
0
votes
2
replies
223
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
0
votes
5
replies
285
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 days ago by
GenoMax
142k • written 3 days ago by
chrisk
• 0
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by
LucisTheFather
• 0
0
votes
0
replies
131
views
select set of intervals that cover a genomic region
GRanges
bed
2 days ago by
ntsopoul
▴ 60
0
votes
1
reply
579
views
scRNAseq quality control weird double curve in nFeature vs nCount plot
scRNA-seq
QC
single
cell
BDRhapsody
analysis
updated 2 days ago by
valdirbarth
▴ 20 • written 12 months ago by
Salomé
• 0
0
votes
9
replies
352
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
0
votes
0
replies
117
views
qPCR gene expression data analysis
qPCR
geneexpression
anova
2 days ago by
ebertomeup
• 0
0
votes
0
replies
113
views
Blog:
The Current State and Future Prospects of Long-Read Sequencing
LRS
2 days ago by
Novogene
▴ 420
181 results • Page
2 of 4
Recent Votes
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
Recent Locations •
All
Iran,
2 minutes ago
United States,
10 minutes ago
South Korea,
12 minutes ago
United States,
14 minutes ago
Morocco,
19 minutes ago
United States,
19 minutes ago
United Kingdom,
20 minutes ago
Recent Awards •
All
Popular Question
to
syedahamdani94
• 0
Popular Question
to
mohammadhassanj
▴ 260
Scholar
to
dsull
★ 6.0k
Popular Question
to
finswimmer
16k
Popular Question
to
Ezequiel
• 0
Popular Question
to
alanh
▴ 170
Scholar
to
Peter
6.0k
Recent Replies
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Traffic: 1410 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