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130 results • Page
2 of 3
Sort: Votes
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Views
Votes
Replies
0
votes
0
replies
205
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
3 days ago by
abhishekghadge
• 0
0
votes
0
replies
128
views
Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation
CGenFF
Gromacs
VMD
3 days ago by
Mamatha Y S
• 0
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria
mauve
genome
3 days ago by
rthapa
▴ 90
0
votes
0
replies
134
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
2
replies
248
views
bam merging for archaic samples
samtools
bam
updated 2 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
114
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
0
replies
74
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
2 days ago by
Biostars2200
• 0
0
votes
0
replies
68
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
0
votes
0
replies
81
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
0
votes
0
replies
66
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
0
votes
0
replies
74
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
0
replies
77
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
2 days ago by
feather-W
• 0
0
votes
1
reply
136
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
77
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
0
votes
1
reply
112
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
0
replies
197
views
traying to make a maf from an already annotated vcf
vcf
vcf2maf
maf
maftools
VEP
2 days ago by
Javier
• 0
0
votes
1
reply
118
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
0
votes
2
replies
172
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Patadu94
• 0
0
votes
0
replies
84
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 1 day ago by
Ram
43k • written 1 day ago by
sansan_96
▴ 80
0
votes
0
replies
131
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 1 day ago by
Ram
43k • written 1 day ago by
Oak
▴ 10
0
votes
0
replies
272
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 1 day ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
2
replies
140
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
0
replies
101
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 1 day ago by
Ram
43k • written 1 day ago by
maxime.policarpo
▴ 200
0
votes
1
reply
129
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 1 day ago by
Ram
43k • written 1 day ago by
Cameron.walker9900
• 0
0
votes
8
replies
266
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
0
votes
0
replies
68
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
0
votes
0
replies
81
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
0
votes
1
reply
122
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
0
replies
70
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 23 hours ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
0
replies
89
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 23 hours ago by
Ram
43k • written 1 day ago by
Amélie
• 0
0
votes
1
reply
114
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 23 hours ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
0
votes
0
replies
66
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
22 hours ago by
ohtang7
▴ 40
0
votes
0
replies
76
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 22 hours ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
1
reply
109
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 19 hours ago by
bk11
★ 2.3k • written 19 hours ago by
alphaflylizard
• 0
0
votes
1
reply
181
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 16 hours ago by
Istvan Albert
100k • written 1 day ago by
qudrat.nii
▴ 10
0
votes
0
replies
58
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
15 hours ago by
Kash
▴ 110
0
votes
10
replies
333
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
11 hours ago by
atowns21
• 0
0
votes
1
reply
95
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 10 hours ago by
Mensur Dlakic
★ 27k • written 16 hours ago by
benguyarenbeyaz98
• 0
0
votes
0
replies
42
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
hetero
Seurat
modelHomotypic
DoubletFinder
8 hours ago by
Jeyong
• 0
0
votes
2
replies
172
views
How to calculate identity percentage between proteins contained in a FASTA file?
percentage
FASTA
alignment
identity
updated 6 hours ago by
b.contreras.moreira
▴ 170 • written 17 hours ago by
v.berriosfarias
▴ 140
0
votes
0
replies
35
views
Network Alignment
plugin
Cytoscape
CytoMCS
6 hours ago by
Akash D
▴ 40
0
votes
0
replies
41
views
Alternative splicing
single-cell
suppa
rnaseq
splicing
alternative
5 hours ago by
newuser2024
• 0
0
votes
6
replies
413
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 5 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
0
votes
0
replies
53
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
4 hours ago by
salias
• 0
0
votes
5
replies
238
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
3 hours ago by
njornet
▴ 20
0
votes
0
replies
26
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
2 hours ago by
mawigoj318
• 0
0
votes
1
reply
67
views
alignment result
RNA-seq
samtool
analysis
hisat2
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
ahmad.sajad4541
• 0
0
votes
2
replies
84
views
different FeatureCounts output for the same data
fpkm
rnaseq
Counts
Rsubread
updated 1 hour ago by
Istvan Albert
100k • written 5 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
12
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
35 minutes ago by
pramach1
▴ 40
0
votes
0
replies
9
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
24 minutes ago by
Bertalan_Takacs
▴ 90
130 results • Page
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Recent Votes
Answer: How to trim transcripts using information from NCBI contamination screen report
Difference Between "Mate Pair" And "Pair-End"
Difference Between "Mate Pair" And "Pair-End"
Comment: To get p-values for the TPM
Comment: HaplotypeCaller - only SNPs
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
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Comment: How to trim transcripts using information from NCBI contamination screen report
by
Lada
▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
Comment: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
mropri
▴ 150
Thank you, will do Wilcox for now as I only have one control and one treatment, as I get more control and treatment samples, will stick wit…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
I think the blog post lines up wit both of our statements. It seems that 2-way binning (pass/fail) already dramatically improves the calls…
Comment: Tax4Fun2 - error
by
drstalinantony28
• 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Windo…
Answer: Tax4Fun2 - error
by
drstalinantony28
• 0
You have to follow this step to solve the issue. (Mostly this problem occurs in the Windows version) 1. If you are using R studio in Win…
Comment: different FeatureCounts output for the same data
by
GenoMax
141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result
by
GenoMax
141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM
by
ATpoint
82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
njornet
▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis
by
gv
• 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM
by
VITALA
• 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM
by
dsull
★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
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