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
110 results • Page
2 of 3
Sort: Views
Rank
Views
Votes
Replies
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
199
views
Lncipedia GTF file error
Proteomics
updated 5 days ago by
Ram
43k • written 5 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
198
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
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
2
replies
191
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 4 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
1
vote
3
replies
188
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
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
1
reply
184
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 1 day ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
183
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
179
views
Chemical structure validation
structure
cap
validation
metabolite
5 days ago by
Rodolfo Adrián
• 0
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 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
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
0
votes
0
replies
172
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
164
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by
ekirsch
• 0
0
votes
0
replies
156
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
1
vote
1
reply
150
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
0
replies
141
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
Oak
▴ 10
0
votes
1
reply
139
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 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
136
views
How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by
Ram
43k • written 3 days ago by
sainavyav22
• 0
0
votes
1
reply
134
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
0
votes
1
reply
132
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 2 days ago by
Cameron.walker9900
• 0
0
votes
2
replies
132
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 4 hours ago by
Ram
43k • written 14 hours ago by
sehriban.buyukkilic
▴ 10
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
1
reply
122
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
0
votes
1
reply
120
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
0
replies
119
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
Atul K.
• 0
0
votes
1
reply
119
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
1
reply
114
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
0
votes
1
reply
108
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 20 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
1
reply
102
views
alignment result
RNA-seq
samtools
hisat2
updated 4 hours ago by
Ram
43k • written 16 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
102
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 2 days ago by
Ram
43k • written 2 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
90
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 1 day ago by
Ram
43k • written 2 days ago by
Amélie
• 0
0
votes
0
replies
90
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
0
votes
1
reply
89
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 8 hours ago by
Sofia
• 0 • written 12 hours ago by
mawigoj318
• 0
0
votes
0
replies
85
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 2 days ago by
Ram
43k • written 2 days ago by
sansan_96
▴ 80
0
votes
0
replies
83
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
0
votes
0
replies
80
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 1 day ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
0
replies
79
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
0
votes
0
replies
78
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 day ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
0
replies
78
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
0
votes
0
replies
78
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
9 hours ago by
pramach1
▴ 40
0
votes
0
replies
78
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
2 days ago by
feather-W
• 0
0
votes
0
replies
76
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
2 days ago by
Biostars2200
• 0
0
votes
0
replies
75
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
0
replies
72
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
14 hours ago by
salias
• 0
0
votes
0
replies
70
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
110 results • Page
2 of 3
Recent Votes
Comment: 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
Poland,
5 minutes ago
United States,
12 minutes ago
Japan,
15 minutes ago
Australia,
15 minutes ago
United States,
21 minutes ago
Canada,
22 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: 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.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Traffic: 1909 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