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520 results • Page
1 of 11
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
60
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
5 hours ago by
HarperReed
• 0
0
votes
2
replies
83
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 2 hours ago by
GenoMax
141k • written 6 hours ago by
sapuizait
▴ 10
1
vote
0
replies
45
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
7 hours ago by
KABILAN
▴ 50
0
votes
0
replies
45
views
Running Phylogenetic Analysis With NCBI Genome
population
genetics
phylogenetic
species
sequencing
8 hours ago by
SineWave
• 0
0
votes
0
replies
44
views
RNA-seq: full length gene
identification
gene
full
length
8 hours ago by
Nargis
• 0
0
votes
0
replies
41
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
10 hours ago by
turcoa1
• 0
0
votes
0
replies
61
views
Designing single-stable RNA molecules
structure
RNA
17 hours ago by
Edna
• 0
0
votes
0
replies
70
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
17 hours ago by
simplitia
▴ 130
0
votes
1
reply
107
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 18 hours ago by
ATpoint
82k • written 19 hours ago by
AaronJaime
• 0
0
votes
0
replies
75
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
21 hours ago by
avocado123
• 0
0
votes
0
replies
65
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
21 hours ago by
Emily
▴ 10
1
vote
0
replies
82
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
21 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
68
views
how to read graph_test output of monocle 3
monocle3
22 hours ago by
synat.keam
▴ 100
0
votes
1
reply
398
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 23 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
83
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
1 day ago by
Aspire
▴ 300
0
votes
2
replies
164
views
Highest variable features in single cell data
single-cell
updated 18 hours ago by
Ram
43k • written 1 day ago by
Kazo
• 0
0
votes
2
replies
195
views
PCA plot
DESeq2
PCAplot
updated 5 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
0
replies
107
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 day ago by
4fzcgueyp5
• 0
0
votes
2
replies
213
views
Annovar using R package
Annovar
gnomAD
R
17 hours ago by
DKA
▴ 40
0
votes
5
replies
291
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 1 day ago by
GenoMax
141k • written 2 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
129
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 2 days ago by
glaciya2018
• 0
0
votes
0
replies
247
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
2 days ago by
pramach1
▴ 40
0
votes
1
reply
140
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 day ago by
Sofia
• 0 • written 2 days ago by
mawigoj318
• 0
0
votes
0
replies
130
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
2 days ago by
salias
• 0
0
votes
4
replies
250
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
1 day ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
112
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 2 days ago by
newuser2024
• 0
1
vote
2
replies
198
views
alignment result
RNA-seq
samtools
hisat2
1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
94
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 day ago by
Ram
43k • written 2 days ago by
Jeyong
• 0
0
votes
0
replies
104
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
2 days ago by
Kash
▴ 110
0
votes
1
reply
144
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
236
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
820
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
470
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
14 hours ago by
atowns21
• 0
0
votes
1
reply
150
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 2 days ago by
bk11
★ 2.4k • written 2 days ago by
alphaflylizard
• 0
0
votes
0
replies
94
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
1
reply
153
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 3 days ago by
GenoMax
141k • written 3 days ago by
Srinka
▴ 20
0
votes
5
replies
290
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
2 days ago by
njornet
▴ 20
0
votes
0
replies
87
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 3 days ago by
SHREYA
• 0
0
votes
0
replies
95
views
Merging replicates from Encode project
CHIP-seq
encode
3 days ago by
Nurken
• 0
1
vote
3
replies
205
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 days ago by
WouterDeCoster
47k
1
vote
3
replies
248
views
some error in building kraken2 database
metagenome
kraken2
2 days ago by
Art1ess
• 0
0
votes
1
reply
130
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 days ago by
bk11
★ 2.4k • written 3 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
166
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 3 days ago by
Kasturi
• 0
0
votes
0
replies
86
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 3 days ago by
SSSJec
• 0
0
votes
1
reply
143
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 3 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
309
views
Error in cnetplot enrichplot package
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
0
votes
0
replies
107
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
92
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
94
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
0
votes
0
replies
197
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
520 results • Page
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Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
Answer: what is the purpose of indexing the reference genome (Kallisto)
by
dsull
★ 5.8k
I'll see if I can explain things in super simple terms (albeit with some abuse of the actual technical details) to provide a conceptual und…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
Jalil Sharif
▴ 80
The updated code in R using rtracklayer for reading a gtf file. https://github.com/jalilsharif/gtf_utr_fix_r/blob/main/gencode_utr_fix_d…
Comment: Rare Disease Variant Pathway Analysis
by
The_PyPanda
▴ 10
Thank you LauferVA, Your advice has been useful and I now a lot to think about and read. Also, I just wanted to clarify I do not ha…
Comment: CDS vs cDNA vs transcript for mapping RNA-Seq reads
by
Antonio R. Franco
★ 5.1k
You cannot do it with Kallisto either. In fact, the indexation will fail in attempting to index a genome file
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