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 : all time
all time
today
this week
this month
this year
119,128 results • Page
1 of 2383
Sort: Rank
Rank
Views
Votes
Replies
0
votes
1
reply
71
views
How to handle RNA seq data with unbalanced % rRNA by group?
fastqscreen
rRNA
DESeq2
RNAseq
DGE
updated 42 minutes ago by
dsull
★ 6.9k • written 15 hours ago by
ev97
▴ 30
1
vote
3
replies
120
views
Forum:
Use of gVCF by clinical sequencing labs
gvcf
updated 3 hours ago by
Jeremy Leipzig
22k • written 7 hours ago by
bdolin
▴ 100
0
votes
0
replies
54
views
genome annotation and GFF file formation
MetaEuk
GFF
whole-genome-annotation
updated 9 hours ago by
Ram
44k • written 9 hours ago by
manaswiniparija3
▴ 40
819
votes
169
replies
156k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 27 days ago by
Biostar
3.0k • written 7.9 years ago by
Istvan Albert
101k
0
votes
0
replies
51
views
how to calculate te RSA values of each residue of a protein using DSSP?
RSA
proteins
updated 8 hours ago by
Ram
44k • written 10 hours ago by
raul enrique
• 0
2
votes
2
replies
194
views
Outlier after DEseq2 in meta-analysis
meta-analysis
rna-seq
outlier
DESeq2
10 hours ago by
astefanovic496
▴ 10
0
votes
0
replies
58
views
Optimizing mutect/sarek for somatic substitution variant calling
mutect2
tumor-normal
sarek
variant-calling
updated 10 hours ago by
Ram
44k • written 11 hours ago by
ramiro.barrantes
• 0
0
votes
1
reply
92
views
Appropriate minimum gene set size for gene set enrichment analysis
HTSanalyzer
gsea
FGSEA
updated 10 hours ago by
Ram
44k • written 12 hours ago by
Bine
▴ 70
0
votes
0
replies
68
views
News:
Course - Introduction to the Analysis of Longitudinal Data in Biology Using R
Longitudinal-Data
R
Epidemiology
Forecasting
Gene-Expression
updated 10 hours ago by
Ram
44k • written 14 hours ago by
carlopecoraro2
★ 2.6k
0
votes
0
replies
61
views
missing data in ChromHMM
ChromHMM
updated 10 hours ago by
Ram
44k • written 14 hours ago by
luminea
▴ 10
1
vote
1
reply
97
views
Help on encode accessions
encode
updated 12 hours ago by
GenoMax
146k • written 15 hours ago by
tsomakiank
▴ 50
1
vote
4
replies
153
views
Choosing the best representative transcript for a gene
transcript
updated 8 hours ago by
Ram
44k • written 15 hours ago by
Biodee
• 0
0
votes
1
reply
89
views
Seurat Xenium QC
R
Xenium
spatial
Seurat
updated 15 hours ago by
Bastien Hervé
5.7k • written 15 hours ago by
yura.grabovska
▴ 530
4
votes
4
replies
181
views
gtf files for various organism in ucsc
gtf
14 hours ago by
1769mkc
★ 1.2k
0
votes
0
replies
76
views
merging of two assemblies from different short-reads techniques
hybrid
illumina
assembly
DNBSEQ
16 hours ago by
Andrew Yu
• 0
0
votes
3
replies
315
views
Issue with Downloading Genomes from BVBRC
BVBRC
genomes
updated 23 hours ago by
GenoMax
146k • written 10 weeks ago by
ryanmaroun3
• 0
1
vote
3
replies
172
views
PyMOL scripting with GPUs on LSF
pymol
hpc
pse
lsf
structure
updated 16 hours ago by
GenoMax
146k • written 1 day ago by
noodle
▴ 590
0
votes
2
replies
233
views
Cluster regions based on similar/dissimilar ChIP-seq signal profile across the whole region and not just overall mean signal.
clustering
chip-seq
deeptools
updated 1 day ago by
Ming Tommy Tang
★ 4.4k • written 1 day ago by
rls_08
▴ 40
3
votes
4
replies
253
views
What is wrong with my scripts?
R
GDC
TCGAbiolinks
Bioconductor
updated 1 day ago by
Ming Tommy Tang
★ 4.4k • written 1 day ago by
nuorain
▴ 30
0
votes
3
replies
215
views
cnvpytor run problem
cnvpytor
updated 16 hours ago by
yura.grabovska
▴ 530 • written 1 day ago by
hamideh
▴ 20
3
votes
6
replies
311
views
PCA for count data
PCA
16 hours ago by
QX
▴ 60
3
votes
2
replies
227
views
cnv_facets run problem
R
cnv_facets
17 hours ago by
hamideh
▴ 20
5
votes
12
replies
351
views
Merge VCF files by chromosome and Across samples
GATK
PICARD
MergeVcf
vcftools
updated 1 day ago by
Pierre Lindenbaum
164k • written 1 day ago by
Maverick
▴ 10
0
votes
0
replies
86
views
News:
Genomic Data Visualisation in R (online course)
Data-Visualisation
Genomic-Data
R
1 day ago by
carlopecoraro2
★ 2.6k
2
votes
9
replies
297
views
miRNA mapping with bowtie2 gives low alignment %
bowtie2
alignment
mirna
1 day ago by
Ant
▴ 30
0
votes
5
replies
244
views
Does mageck-vispr calculate differently than mageck?
mageck
mageck-vispr
pooled-screen
cripsr
updated 10 hours ago by
jared.andrews07
★ 17k • written 1 day ago by
Assa Yeroslaviz
★ 1.9k
0
votes
3
replies
185
views
What does fully overlapping supplementary alignments mean?
Alignment
nanopore
minimap2
updated 1 day ago by
Michael
55k • written 1 day ago by
njornet
▴ 20
0
votes
1
reply
139
views
Germline variants in Cancer
Cancer
Tumor-normal
Germline-variant
updated 1 day ago by
Ram
44k • written 1 day ago by
prs
▴ 10
0
votes
7
replies
348
views
Unexplainable missing values in single cell Seurat object
seurat
single-cell
updated 4 hours ago by
Ram
44k • written 1 day ago by
Gerard
▴ 10
2
votes
2
replies
267
views
why do I get this error while reading single cell RNA seq data in R
scRNA-seq
updated 1 day ago by
ATpoint
85k • written 2 days ago by
nuorain
▴ 30
0
votes
2
replies
155
views
Converting ICGC ids to TCGA format
cancer
tcga
icgc
updated 1 day ago by
Ram
44k • written 1 day ago by
hadas.samuels
• 0
0
votes
0
replies
85
views
Comparison of biodiversity between two locations with a known maximum number of species
shannon
ecologie
statistics
biodiversity
1 day ago by
y.
• 0
2
votes
4
replies
335
views
Boxplot with adjustment for variable
R
boxplot
updated 1 day ago by
zx8754
12k • written 4 days ago by
Bine
▴ 70
1
vote
0
replies
131
views
What is the right choice of normalization and preprocessing before WGCNA using RNAseq data in a cohort?
normalization
RNA_seq
cohort
WGCNA
1 day ago by
sukeshinik5
▴ 50
2
votes
5
replies
1.4k
views
VCF file generated by Gridss not recognised by VEP
NGS
variant-calling
VEP
Gridss
updated 1 day ago by
Sunnywy0808
• 0 • written 19 months ago by
Reda
• 0
0
votes
1
reply
319
views
What is more important for Structural Variant Calling? Recall or Precision?
structural-variants
merging
precision-recall
updated 1 day ago by
GenoMax
146k • written 6 months ago by
Luke
• 0
1
vote
2
replies
219
views
Reference genome size for genome size estimation.
genome-size
updated 1 day ago by
Ram
44k • written 2 days ago by
Shakunthala Natarajan
• 0
1
vote
2
replies
263
views
Unexpected High T-Base Content in scRNA-seq Fastq Files and GC Bias Correction
Fastq
Fastqc
scRNA-seq
quality-control
1 day ago by
Cooper
• 0
4
votes
4
replies
377
views
Which Should Take Priority When Selecting DEGs: FDR or Log Fold Change?
DESeq2
logFC
FDR
DEGs
edgeR
16 hours ago by
bioinfo1994
▴ 10
0
votes
3
replies
485
views
batch correction limma package (bead based assay data)
batch-correction
updated 2 days ago by
ATpoint
85k • written 7 days ago by
MC_J
• 0
7
votes
5
replies
3.0k
views
Limma: is it necessary to log-transform the data?
proteomics
limma
updated 2 days ago by
MC_J
• 0 • written 18 months ago by
eodmacmd
• 0
3
votes
9
replies
619
views
I need help with this R script. Thanks.
R
updated 1 day ago by
Ram
44k • written 3 days ago by
nuorain
▴ 30
1
vote
2
replies
301
views
Illumina RNA-seq: Overrepresented sequences are mostly in the R2 reads, not R1
illumina
rRNA
RNAseq
RNA
updated 3 days ago by
GenoMax
146k • written 4 days ago by
Umberto
▴ 10
2
votes
3
replies
369
views
Using DNA Methylation Data as Input for ChromHMM
ChromHMM
methylation
DNA
1 day ago by
luminea
▴ 10
0
votes
0
replies
197
views
A question with interpreting heatmaps from limma
RNA-seq
limma
updated 2 days ago by
Ram
44k • written 4 days ago by
lhwh1208
• 0
0
votes
2
replies
265
views
STRUCTURE runs failing: core dumping and slurm exit code 10?
slurm
linux
STRUCTURE
5 hours ago by
katherinedrotos
• 0
0
votes
0
replies
195
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics
taxonomy
mag
annotation
4 days ago by
LuciaNhu
• 0
1
vote
1
reply
247
views
Comparing whole transcriptome under one condition to the transcriptomes under other conditions
transcriptomics
updated 1 day ago by
dthorbur
★ 2.5k • written 4 days ago by
Texx
• 0
0
votes
0
replies
204
views
News:
Machine Learning for Multi-Omics Integration (online course) -January 13-15, 2025
Machine-Learning
Big-Data
Multi-Omics
Data-Integration
Deep-Learning
updated 2 days ago by
Ram
44k • written 4 days ago by
carlopecoraro2
★ 2.6k
2
votes
1
reply
248
views
How to make DiffBind Run Faster?
DiffBind
ATAC-seq
updated 4 days ago by
jared.andrews07
★ 17k • written 4 days ago by
B.N.
▴ 10
119,128 results • Page
1 of 2383
Recent Votes
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
Use of gVCF by clinical sequencing labs
Overlapping And Unique Peaks In Chipseq
Overlapping And Unique Peaks In Chipseq
A: Calculating percentage of reads mapped to a reference genome
Answer: What does secondary (and some other fields) mean in flagstat output?
Recent Locations •
All
United States,
21 minutes ago
Japan,
22 minutes ago
Boston,
23 minutes ago
Australia,
33 minutes ago
UCLA,
44 minutes ago
United States,
1 hour ago
United States,
1 hour ago
Recent Awards •
All
Popular Question
to
a615ebfb
▴ 40
Popular Question
to
bdolin
▴ 100
Popular Question
to
Maxine
▴ 50
Centurion
to
yura.grabovska
▴ 530
Popular Question
to
firestar
★ 1.6k
Popular Question
to
manaswiniparija3
▴ 40
Popular Question
to
dieunelderilus
▴ 10
Recent Replies
Answer: How to handle RNA seq data with unbalanced % rRNA by group?
by
dsull
★ 6.9k
Just remove the rRNA. No need to add a covariate. You can consider those rRNA differences "biological variation". I'd only use a covaria…
Comment: Use of gVCF by clinical sequencing labs
by
Jeremy Leipzig
22k
gVCF allows you to distinguish no-calls from reference in single samples. as a terminal format it's useful but maybe not essential.
Comment: Use of gVCF by clinical sequencing labs
by
Jeremy Leipzig
22k
I think the bigger trend is the slow death of joint variant calling favor of single-sample variant calling. When I see bp_resolution used i…
Comment: Use of gVCF by clinical sequencing labs
by
Ram
44k
AFAIK clinical labs don't even use VCF files. It's too technical for them. They'd probably have someone extract a tabular file that they ca…
Comment: Trouble with Biopython residue depth
by
Wayne
★ 2.0k
To put things on an even plane with complete code: I simplified to a single chain small protein and that works using the PDB parser. Her…
Comment: STRUCTURE runs failing: core dumping and slurm exit code 10?
by
katherinedrotos
• 0
Thanks for your reply. Yes I checked the logs for STRUCTURE, there are no errors there, it just stops writing at some point. I'm using par…
Comment: Single-cell RNA differential expression with an unbalanced number of cells betwe
by
Javi.villegas21
• 0
Thanks! I just realized that grouping the cells as a major subtype or into the minor subtypes that make up the major does change the number…
Comment: Choosing the best representative transcript for a gene
by
Ram
44k
Maybe the later versions have corrected but canonical defaults to the longest, atleast using snpEff. VEP seems to handle this better. I do …
Comment: validation approach for CNVs
by
heureuse
• 0
Mendelian Precision is an approach i wanted to use but i'm no longer using it.
Comment: Does mageck-vispr calculate differently than mageck?
by
jared.andrews07
★ 17k
Presumably, but I haven't dug through the source code to verify. OP, can you post the full logs from your `vispr` call? And the commands yo…
Comment: how to calculate relative solvent accessibility of all human lysine residues?
by
raul enrique
• 0
can someone explain this step by step please?
Comment: Choosing the best representative transcript for a gene
by
ATpoint
85k
The canonical is not always the longest transcript. I support the suggestion to do gene level analysis. Meaning, use something like tximpo…
Comment: Outlier after DEseq2 in meta-analysis
by
astefanovic496
▴ 10
Dear i.sudbery, Thank you for your response and valuable input! I had some additional thoughts. As I am using the ESTIMATE algorithm to …
Comment: Choosing the best representative transcript for a gene
by
Ram
44k
What Michael said. You have a few options: You can pick the "canonical" = longest transcript, or you can use something like MANE to pick th…
Answer: Appropriate minimum gene set size for gene set enrichment analysis
by
yura.grabovska
▴ 530
This is very much an empirically defined parameter. It would make sense to benchmark within your data. Luckingly methods built on top of fg…
Traffic: 1226 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