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
182 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
6
votes
4
replies
303
views
Details on salmon index
Salmon
updated 1 day ago by
Rob
6.6k • written 2 days ago by
Lorenzo
• 0
1
vote
4
replies
302
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 8 hours ago by
Joe
21k • written 9 days ago by
cput
• 0
2
votes
4
replies
298
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
3 days ago by
Esraa
• 0
3
votes
4
replies
294
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq
patch
freeze
genome
updated 1 day ago by
Jeremy Leipzig
22k • written 2 days ago by
Ali
• 0
0
votes
4
replies
291
views
How to extract cells of different species after mapping with combined genome?
snRNA-seq
scRNA-seq
updated 1 day ago by
Tony
• 0 • written 2 days ago by
vk
▴ 10
1
vote
4
replies
290
views
Add stats to boxplot in R
stats
R
3 days ago by
Ghada
• 0
2
votes
3
replies
290
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
5 days ago by
Azra
▴ 10
0
votes
4
replies
286
views
Merge clusters in Seurat UMAP
seurat
umap
1 day ago by
kilcdincer
▴ 10
3
votes
2
replies
286
views
imputation through beagle
panel
beagle
reference
imputation
4 days ago by
analyst
▴ 50
0
votes
5
replies
286
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
1
vote
3
replies
285
views
Using ggplotly in R
ggplot
ggplotly
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
jen
▴ 10
1
vote
4
replies
285
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
2 days ago by
Arton
▴ 10
0
votes
5
replies
282
views
calculating genomic coverage/ base overlap in R
genomics
updated 6 hours ago by
1769mkc
★ 1.2k • written 3 days ago by
Xbox_27
• 0
0
votes
6
replies
279
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
22 hours ago by
hannes.bongartz
• 0
1
vote
5
replies
278
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
2
votes
3
replies
278
views
Finding variants within a subset of a BAM file
variant
calling
4 days ago by
ramiro.barrantes
• 0
2
votes
5
replies
275
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 4 days ago by
Philipp Bayer
8.5k • written 4 days ago by
林明德
• 0
1
vote
3
replies
274
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 2 days ago by
GenoMax
142k • written 4 days ago by
ohtang7
▴ 40
0
votes
4
replies
272
views
How to handle duplicated genes in TCGA data?
TCGA
GDC
mRNA
updated 10 hours ago by
txema.heredia
▴ 130 • written 1 day ago by
Ngrin
• 0
3
votes
3
replies
271
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 4 days ago by
Ram
43k • written 18 days ago by
Adyasha
• 0
2
votes
4
replies
271
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell
seurat
10XGenomics
scRNAseq
updated 3 days ago by
yura.grabovska
▴ 90 • written 3 days ago by
ev97
▴ 20
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
4 days ago by
Lukas
• 0
0
votes
4
replies
268
views
how to treat the replicates while performing WGCNA
clustering
WGCNA
replicates
11 hours ago by
mavy
▴ 10
1
vote
5
replies
265
views
Annotating file using bcftools
annotation
plink
bcftools
2 days ago by
kl
▴ 10
0
votes
3
replies
264
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
doramora
▴ 10
0
votes
1
reply
264
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 1 day ago by
GenoMax
142k • written 1 day ago by
huxiangyulove
• 0
2
votes
1
reply
264
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 6 days ago by
pjb39
▴ 210 • written 8 days ago by
beantkapoor16
▴ 10
0
votes
4
replies
262
views
Galaxy StringTie error
stringtie
galaxy
4 days ago by
trkfs
• 0
1
vote
3
replies
261
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
0
votes
3
replies
259
views
Sam file Header problem
Sam
Header
problem
file
updated 1 day ago by
Pierre Lindenbaum
161k • written 2 days ago by
saifulislam99121
• 0
3
votes
1
reply
258
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 3 days ago by
dariober
14k • written 4 days ago by
Holly
▴ 30
1
vote
1
reply
247
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
2 days ago by
ramiro.barrantes
• 0
0
votes
1
reply
247
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 4 days ago by
Ram
43k • written 9 days ago by
Nikki
• 0
2
votes
3
replies
246
views
ggrepel function: geom_text_repel()
ggplot2
ggrepel
R
updated 1 day ago by
Ram
43k • written 2 days ago by
sooni
▴ 20
0
votes
1
reply
244
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 8 days ago by
jain72744
▴ 10
0
votes
4
replies
241
views
Sequencing Depth (Read Depth) Calculations
depth
2 days ago by
LucisTheFather
• 0
0
votes
2
replies
235
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
5 days ago by
analyst
▴ 50
0
votes
1
reply
234
views
input file in rmats
rmats
updated 6 days ago by
Mathew
▴ 140 • written 8 days ago by
Lambodarswain316
• 0
0
votes
2
replies
233
views
Obtaining Infinium Methylation450K manifest for hg38
TCGA
hg38
methylation
Illumina
updated 5 days ago by
Zhenyu Zhang
★ 1.2k • written 10 days ago by
elisheva
▴ 120
2
votes
4
replies
230
views
Help with IGV abbreviation
igv
updated 3 days ago by
Ram
43k • written 4 days ago by
GeneC
• 0
3
votes
3
replies
229
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Alexandra
• 0
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
2
votes
2
replies
225
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 1 day ago by
Ram
43k • written 2 days ago by
txema.heredia
▴ 130
1
vote
2
replies
225
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
2 days ago by
MarcosCosta
• 0
0
votes
2
replies
223
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
2 days ago by
Chen
• 0
1
vote
5
replies
219
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
3
votes
1
reply
218
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 5 days ago by
aw7
▴ 300 • written 9 days ago by
Zeng Hao
▴ 40
2
votes
3
replies
215
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 3 days ago by
Ram
43k • written 3 days ago by
Prawesh
• 0
3
votes
3
replies
215
views
getting exon coordinates
genomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Xbox_27
• 0
0
votes
3
replies
215
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 4 days ago by
GenoMax
142k • written 4 days ago by
RNAseqer
▴ 270
182 results • Page
2 of 4
Recent Votes
Answer: RNAseq coverage vs depth for transcript isoform expression?
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
Recent Locations •
All
Bologna,
2 minutes ago
United States,
6 minutes ago
United States,
17 minutes ago
United States,
18 minutes ago
United States,
24 minutes ago
Machhagan,
25 minutes ago
United States,
29 minutes ago
Recent Awards •
All
Scholar
to
jv
★ 1.8k
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
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: 1269 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