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
1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
5
replies
426
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
0
replies
136
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by
Ram
43k • written 4 days ago by
sainavyav22
• 0
0
votes
0
replies
137
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
4 days ago by
rthapa
▴ 90
0
votes
0
replies
131
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
4 days ago by
Mamatha Y S
• 0
0
votes
2
replies
251
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
1
vote
0
replies
536
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
4 days ago by
mathavanbioinfo
▴ 90
0
votes
0
replies
209
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
4 days ago by
abhishekghadge
• 0
2
votes
5
replies
674
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
0
votes
0
replies
184
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 5 days ago by
Ram
43k • written 5 days ago by
mja
• 0
0
votes
0
replies
186
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
5 days ago by
Nitin
• 0
0
votes
0
replies
186
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by
Ram
43k • written 5 days ago by
yifangt86
▴ 60
0
votes
0
replies
179
views
Chemical structure validation
structure
cap
validation
metabolite
5 days ago by
Rodolfo Adrián
• 0
0
votes
1
reply
258
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
0
votes
0
replies
202
views
Copy number variation plot
Copy-number-variation
genomics
updated 5 days ago by
Ram
43k • written 5 days ago by
Emmi
• 0
0
votes
0
replies
175
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
5 days ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
278
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
0
votes
0
replies
193
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 5 days ago by
Ram
43k • written 5 days ago by
Dinmukhamed
• 0
0
votes
0
replies
192
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by
Atul K.
• 0
0
votes
0
replies
199
views
Lncipedia GTF file error
Proteomics
updated 5 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
3
votes
3
replies
461
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 4 days ago by
swbarnes2
14k • written 5 days ago by
joe
▴ 510
0
votes
2
replies
531
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
6 days ago by
航太郎
• 0
0
votes
0
replies
210
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by
GenoMax
141k • written 6 days ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
370
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
5 days ago by
Ashok
• 0
0
votes
2
replies
409
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
5 days ago by
Ashok
• 0
0
votes
0
replies
210
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 6 days ago by
Ram
43k • written 6 days ago by
samuelkalandarov2002
▴ 10
0
votes
2
replies
417
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
0
votes
0
replies
199
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
2 days ago by
Javier
• 0
0
votes
0
replies
174
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
6 days ago by
enferdeflame
• 0
1
vote
1
reply
410
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 6 days ago by
Chris
▴ 260
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 6 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
0
replies
157
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score
tspex
updated 6 days ago by
Ram
43k • written 6 days ago by
bioinfo223
▴ 10
0
votes
0
replies
173
views
How to root an unrooted tree with a known root tree?
phylogenetics
rooting
R
6 days ago by
P.
• 0
0
votes
0
replies
165
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by
ekirsch
• 0
1
vote
1
reply
388
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 days ago by
renan.igor
• 0
0
votes
0
replies
173
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
7 days ago by
synat.keam
▴ 100
0
votes
1
reply
264
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 7 days ago by
GenoMax
141k • written 7 days ago by
ycts
• 0
0
votes
4
replies
572
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
5 days ago by
Kai Xin
• 0
1
vote
1
reply
222
views
Retrieve a % coverage for each transcript
RNA-seq
updated 7 days ago by
Ram
43k • written 7 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
365
views
How can I solve this error?
metal
6 days ago by
22211020193
• 0
0
votes
0
replies
164
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 7 days ago by
GenoMax
141k • written 7 days ago by
srimmer
• 0
1
vote
2
replies
268
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 7 days ago by
Ram
43k • written 7 days ago by
aniigodwinn
• 0
0
votes
0
replies
352
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
7 days ago by
Ronin
• 0
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
0
votes
1
reply
194
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 7 days ago by
DKA
▴ 40 • written 7 days ago by
james.melhorn
• 0
0
votes
1
reply
181
views
Freyja plot error
Freyja
updated 7 days ago by
Ram
43k • written 7 days ago by
Adyasha
• 0
0
votes
0
replies
154
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
7 days ago by
chemokine-1
▴ 10
0
votes
4
replies
491
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
6 days ago by
feather-W
• 0
0
votes
2
replies
216
views
Bedmethyl file format
bedmethyl
methylation
updated 7 days ago by
GenoMax
141k • written 7 days ago by
njornet
▴ 20
0
votes
0
replies
167
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
7 days ago by
Ali
• 0
2
votes
4
replies
309
views
SnpEff annotates coding duplication as intronic?
snpeff
7 days ago by
kirill.zaslavsky
• 0
1,000 results • Page
2 of 20
Recent Votes
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
Recent Locations •
All
United States,
1 minute ago
Republic of Ireland,
8 minutes ago
China,
12 minutes ago
United States,
15 minutes ago
South Korea,
21 minutes ago
USA,
21 minutes ago
United States,
24 minutes ago
Recent Awards •
All
Popular Question
to
Simone
▴ 10
Popular Question
to
carlopecoraro2
★ 2.5k
Popular Question
to
daffodil
▴ 10
Popular Question
to
Russ
▴ 500
Popular Question
to
camillab.
▴ 160
Popular Question
to
pramach1
▴ 40
Popular Question
to
Adyasha
• 0
Recent Replies
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Traffic: 2015 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