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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
402
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
6 days ago by
renan.igor
• 0
0
votes
0
replies
177
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
8 days ago by
synat.keam
▴ 100
0
votes
1
reply
268
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 8 days ago by
GenoMax
141k • written 8 days ago by
ycts
• 0
0
votes
4
replies
577
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
7 days ago by
Kai Xin
• 0
1
vote
1
reply
225
views
Retrieve a % coverage for each transcript
RNA-seq
updated 8 days ago by
Ram
43k • written 8 days ago by
jammydodger123456
▴ 40
0
votes
2
replies
369
views
How can I solve this error?
metal
8 days ago by
22211020193
• 0
0
votes
0
replies
166
views
Struggling to lift genome builds
PLINK
liftover
GWAS
updated 8 days ago by
GenoMax
141k • written 8 days ago by
srimmer
• 0
1
vote
2
replies
273
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 8 days ago by
Ram
43k • written 8 days ago by
aniigodwinn
• 0
0
votes
0
replies
354
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
9 days ago by
Ronin
• 0
2
votes
7
replies
815
views
Removing duplicates
duplicates
ONT
minimap2
updated 7 days ago by
joe
▴ 510 • written 9 days ago by
quentinperriere
• 0
0
votes
1
reply
196
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 9 days ago by
DKA
▴ 40 • written 9 days ago by
james.melhorn
• 0
0
votes
1
reply
185
views
Freyja plot error
Freyja
updated 8 days ago by
Ram
43k • written 9 days ago by
Adyasha
• 0
0
votes
0
replies
156
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
9 days ago by
chemokine-1
▴ 10
0
votes
4
replies
502
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
8 days ago by
feather-W
• 0
0
votes
2
replies
224
views
Bedmethyl file format
bedmethyl
methylation
updated 9 days ago by
GenoMax
141k • written 9 days ago by
njornet
▴ 20
0
votes
0
replies
168
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
9 days ago by
Ali
• 0
2
votes
4
replies
316
views
SnpEff annotates coding duplication as intronic?
snpeff
9 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
248
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
9 days ago by
mropri
▴ 150
0
votes
0
replies
143
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
9 days ago by
shasabhi1
• 0
0
votes
0
replies
133
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
9 days ago by
Nishat
• 0
0
votes
0
replies
160
views
what exactly is a k-mer table (remora)?
remora
basecall
9 days ago by
anne
• 0
1
vote
1
reply
179
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 9 days ago by
dsull
★ 5.8k • written 9 days ago by
niruf
• 0
0
votes
0
replies
143
views
GWAS Phenotypes
GWAS
10 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
317
views
GSEA analysis in R
GSEA
R
Arabidopsis
8 days ago by
Sudip
• 0
0
votes
0
replies
122
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
10 days ago by
QX
• 0
2
votes
5
replies
444
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
9 days ago by
Bikram Kumar
• 0
0
votes
2
replies
258
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 9 days ago by
Ram
43k • written 10 days ago by
David
• 0
1
vote
2
replies
267
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
9 days ago by
bioinfo
▴ 150
0
votes
1
reply
192
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 10 days ago by
bk11
★ 2.4k • written 10 days ago by
sinhas
• 0
0
votes
1
reply
208
views
merging Seurat objects after SCT
Seurat
SCT
updated 10 days ago by
Ram
43k • written 10 days ago by
michelle.swarovski
• 0
0
votes
1
reply
203
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 10 days ago by
GenoMax
141k • written 10 days ago by
haiying.kong
▴ 360
0
votes
2
replies
264
views
RNAseq 1 control 2 different treatment
RNA-seq
10 days ago by
matteo.levorato
• 0
1
vote
0
replies
143
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 10 days ago by
Ram
43k • written 10 days ago by
Oscar
▴ 10
0
votes
0
replies
153
views
How should I make kallisto indexes?
kallisto
updated 11 days ago by
GenoMax
141k • written 11 days ago by
bioinfo
▴ 150
2
votes
0
replies
205
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
11 days ago by
Alexander
▴ 220
1
vote
1
reply
181
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 11 days ago by
GenoMax
141k • written 11 days ago by
eesiribloom
▴ 80
0
votes
0
replies
137
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
11 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
142
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
11 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
151
views
FreeBayes detection capacity
reads
freebayes
long
11 days ago by
quentinperriere
• 0
0
votes
2
replies
247
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
9 days ago by
DKA
▴ 40
0
votes
0
replies
161
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
11 days ago by
Hien
• 0
0
votes
2
replies
286
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
9 days ago by
Koketso
• 0
0
votes
0
replies
189
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 11 days ago by
Ram
43k • written 12 days ago by
menyawino
• 0
1
vote
3
replies
347
views
Ensembl gene id conversion
biomart
ensembl
updated 10 days ago by
ATpoint
82k • written 12 days ago by
naveedhasan2000
• 0
1
vote
2
replies
315
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 10 days ago by
Istvan Albert
100k • written 12 days ago by
Jiang
• 0
0
votes
0
replies
192
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
13 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
316
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
12 days ago by
O.rka
▴ 710
0
votes
6
replies
548
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
10 days ago by
Dunois
★ 2.5k
4
votes
7
replies
550
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 12 days ago by
Ram
43k • written 13 days ago by
AHerik
▴ 20
0
votes
0
replies
187
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 13 days ago by
GenoMax
141k • written 13 days ago by
zec018
• 0
1,000 results • Page
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Recent Replies
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely mapping in regions whe…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
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…
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