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1,526 results • Page
1 of 31
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How to find the most frequent alternative-splicing event from DEXSEQ data?
DESEQ
RNA-SEQ
DEXSEQ
just now by
STARDUST
• 0
0
votes
0
replies
1
view
How to use CAFE from Orthofinder Results
expansion
orthofinder
cafe
gene
just now by
ahmadjoyyia
• 0
0
votes
1
reply
76
views
To batch correct or analyse separately?
scRNA-seq
batch
correction
updated 1 hour ago by
ATpoint
68k • written 10 hours ago by
bompipi95
▴ 50
1
vote
2
replies
72
views
Issue with hmmcalibrate during tutorial.
hmmsearch
hmmbuild
hmmer
hmmcalibrate
9 minutes ago by
apcreyes29
• 0
0
votes
0
replies
65
views
SNP calling
SNPcalling
3 hours ago by
abozorgmehr1985
• 0
0
votes
0
replies
56
views
News:
Course - INTRODUCTION TO PYTHON PROGRAMMING FOR BIOLOGISTS
Bioinformatics
Programming
Python
4 hours ago by
carlopecoraro2
★ 2.2k
2
votes
2
replies
190
views
How to merge unique/non overlapping genes between 2 gene model GFF3 files?
gff3
updated 7 hours ago by
Juke34
7.5k • written 23 hours ago by
William
★ 5.1k
0
votes
0
replies
64
views
gistic- overlapp
CNV
GISTIC
TCGA
8 hours ago by
Hanie
• 0
0
votes
0
replies
85
views
Protocol to detect chromosomal ploidy from WGS VCF?
wgs
ploidy
15 hours ago by
optimistsso4co3
▴ 100
0
votes
1
reply
107
views
Obtaining every"Protein ID" from a genome in OMA
OMA
orthologs
updated 15 hours ago by
clement.train
▴ 40 • written 17 hours ago by
christyh
• 0
0
votes
0
replies
75
views
SpliceAi same variant , different score
SpliceAi
updated 16 hours ago by
Pierre Lindenbaum
152k • written 16 hours ago by
vvasta
• 0
0
votes
1
reply
123
views
Diffbind losing peaks when going from small to larger consensus peak set
DiffBind
14 hours ago by
tara.mcintyre
• 0
0
votes
0
replies
85
views
GSEA multiple group analysis
gsea
single-cell
18 hours ago by
piotto
▴ 10
0
votes
0
replies
101
views
want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
DEGs
updated 19 hours ago by
ATpoint
68k • written 19 hours ago by
rupali
• 0
0
votes
1
reply
134
views
RNA Editing data from RNA-seq
Editing
RNA
updated 19 hours ago by
Juke34
7.5k • written 19 hours ago by
Genetics
• 0
0
votes
2
replies
145
views
cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
bcl2fastq
cellranger-arc
mkfastq
cellranger
19 hours ago by
Yingying
• 0
0
votes
0
replies
106
views
Unrooted consensus tree [Bio.Phylo]
consensus
phylo
biopython
21 hours ago by
Jimpix
▴ 10
0
votes
0
replies
86
views
PLINK2 selecting variants based on INFO score
plink2
22 hours ago by
m.c.roozen
• 0
0
votes
3
replies
192
views
DESeq2 results function runs very slow on Windows 10
r
deseq2
updated 21 hours ago by
ATpoint
68k • written 23 hours ago by
Taha
• 0
1
vote
2
replies
147
views
How can I convert this pairwise format to fasta?
fasta
python
bash
updated 19 hours ago by
GenoMax
125k • written 23 hours ago by
SaltedPork
▴ 170
0
votes
2
replies
185
views
Trimmomatic
Trimmomatic
RNA
quality-check
updated 22 hours ago by
Ram
37k • written 1 day ago by
Monia
• 0
0
votes
0
replies
72
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
1 day ago by
bioinfo
▴ 20
1
vote
2
replies
128
views
When you convert a BAM back into a FastQ do you get the original Fastq?
bam
FastQ
updated 1 day ago by
GenoMax
125k • written 1 day ago by
louis-gil
• 0
3
votes
6
replies
233
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot
Volcano
16 hours ago by
Chris
▴ 60
0
votes
1
reply
83
views
Converting large GSM from GEOquery into a minfi or limma workable set
minfi
methylation
limma
GEOquery
R
updated 1 day ago by
Basti
★ 1.3k • written 1 day ago by
Edward E-B
• 0
1
vote
1
reply
91
views
bwa mem duration?
performance
mapping
bwa
updated 1 day ago by
ATpoint
68k • written 1 day ago by
lacb
▴ 30
8
votes
9
replies
2.6k
views
7 follow
Translating gene names to entrez id's
database
annotation
biopython
gene
python
updated 23 hours ago by
Ram
37k • written 22 months ago by
Julian
• 0
0
votes
1
reply
122
views
Gene ontology with locus tags
ontology
locus
gene
tags
updated 1 day ago by
dthorbur
▴ 260 • written 1 day ago by
sea.joson
▴ 10
3
votes
4
replies
278
views
High downstream gene expression
downstream
High
Gene
expression
5 hours ago by
yoser4
▴ 10
0
votes
1
reply
132
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 1 day ago by
andres.firrincieli
3.1k • written 1 day ago by
harish
• 0
0
votes
6
replies
237
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 1 day ago by
GenoMax
125k • written 1 day ago by
luzglongoria
▴ 40
2
votes
4
replies
293
views
Annotating ENS codes to gene name
expression
RNA-seq
DEseq2
updated 5 hours ago by
Apex92
▴ 250 • written 1 day ago by
yoosefyud
▴ 40
0
votes
5
replies
327
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
updated 6 hours ago by
barslmn
★ 1.2k • written 1 day ago by
ibq.enriquepola
• 0
0
votes
0
replies
100
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
1 day ago by
manaswiniparija3
▴ 10
0
votes
1
reply
155
views
Using Entrez Utilities to query the Nucleotide database by collection_date
ncbi
entrez
updated 1 day ago by
GenoMax
125k • written 1 day ago by
anomalous.lexeme
• 0
0
votes
0
replies
109
views
scATAC merging of files
Signac
scATAC-seq
1 day ago by
bioinformatics.girl
• 0
0
votes
1
reply
175
views
Manual Polygenic Risk Score calculation
calculation
steps
PRS
updated 1 day ago by
Sam
★ 4.6k • written 1 day ago by
Roy
▴ 10
4
votes
4
replies
328
views
2D structure of a custom protein (not in any databases) from a PDB file.
Tool
Pymol
PDB
protein
structure
updated 1 day ago by
Jiyao Wang
▴ 290 • written 2 days ago by
Hansen_869
▴ 50
0
votes
0
replies
118
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
1 day ago by
anubratadas
▴ 20
0
votes
0
replies
137
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
1 day ago by
bioinfo
▴ 20
0
votes
0
replies
121
views
VNTR genotyping
NGS
VNTR
genotyping
1 day ago by
Genotepes
▴ 950
0
votes
0
replies
112
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
1 day ago by
CH1374
▴ 10
0
votes
3
replies
225
views
Faking hh-suite workflow / alignment output
alignment
hhsuite
updated 1 day ago by
Mensur Dlakic
★ 22k • written 1 day ago by
Nick
▴ 40
0
votes
4
replies
300
views
RNASeq differential expression masked by pathways disregulation
normalization
Rnaseq
batch
updated 1 day ago by
i.sudbery
16k • written 1 day ago by
Gama313
▴ 110
0
votes
0
replies
113
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
1 day ago by
a.bibek52
• 0
0
votes
0
replies
112
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
1 day ago by
a.bibek52
• 0
0
votes
1
reply
170
views
Create a new seurat object using one cluster identified in a previous seurat object
object
seurat
Create
clusterization
updated 1 day ago by
Ribo
▴ 20 • written 1 day ago by
Fernanda
• 0
4
votes
2
replies
206
views
Analyzing bulk RNA-seq
RNAseq
updated 1 day ago by
swbarnes2
13k • written 1 day ago by
Zaid
• 0
0
votes
5
replies
234
views
Why am I getting only one common value when comparing two excel files?
python
pandas
excel
updated 1 day ago by
seidel
10k • written 1 day ago by
namck
• 0
2
votes
4
replies
287
views
Alien-hunter outputs
alien-hunter
21 hours ago by
schlogl
▴ 130
1,526 results • Page
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Answer: Issue with hmmcalibrate during tutorial.
Over Representation Vs Enrichment Analysis
Answer: Using Seurat function `FindMarkers` to find differentially expressed genes betwe
C: Which genome files to use for STAR?
Answer: Remove mitochondrial reads from BAM files
Comment: translate CDS to prot formatted with nt nubers
Comment: Analyzing bulk RNA-seq
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Recent Replies
Comment: phylogeny
by
炫
• 0
Hello, my problem is the same as yours, did you finally solve this problem?
Comment: phylogeny
by
炫
• 0
您好,我的问题和您的一模一样,请问您这个问题最终解决了吗
Comment: Issue with hmmcalibrate during tutorial.
by
apcreyes29
• 0
If that's the case then I'll just proceed then. Thank you!
Answer: To batch correct or analyse separately?
by
ATpoint
68k
Instead of writing that all down I recommend to read the relevant part of the Bioconductor scRNA-seq book (OSCA) which covers the "how's" a…
Answer: Issue with hmmcalibrate during tutorial.
by
Mensur Dlakic
★ 22k
Pretty sure that `hmmcalibrate` does not exist in HMMer version 3+ as the models are internally calibrated. I think you are using a manual …
Comment: High downstream gene expression
by
yoser4
▴ 10
Thank you for your reply. Your answer has helped me. I am a novice in scientific research, and the reading of literature is really poor. …
Comment: High downstream gene expression
by
yoser4
▴ 10
Thank you for your reply. Sorry, there are some omissions in the information. This is my problem. First of all, the species I study is shee…
Comment: Annotating ENS codes to gene name
by
Apex92
▴ 250
you can use `merge` function in R to do this. It is quite straight forward.
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
[It looks like “?” is a valid character for the strand column][1]. There are only 5 "?" in that gff file, you can just change it using a te…
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
by
Juke34
7.5k
agat_sp_complement_annotations.pl From [AGAT][1] does the job also. It allows different loci of coding gene to overlap at their UTR levels…
Comment: Annotating ENS codes to gene name
by
yoosefyud
▴ 40
Thank for your points. I created a data frame from my .gtf file using rtracklayer package. Can you please tell the command I should use in…
Comment: Diffbind losing peaks when going from small to larger consensus peak set
by
tara.mcintyre
• 0
I'm now realizing it might be due to the filter parameter being set =1 when I run dba.count because when I set it to 0, all of the peaks ar…
Answer: Obtaining every"Protein ID" from a genome in OMA
by
clement.train
▴ 40
Hello, It seems that the current download is limited to 100 genes on the genomes pages, we will increase this limit to the extent of ea…
Comment: DNA methylation (RRBS/WGBS) prediction from DNA sequence (WGS)
by
Lalaland
▴ 10
Thank you very much, Matthias! I will definitely check those links out myself!
Comment: RNA Editing data from RNA-seq
by
Juke34
7.5k
What tool did you look at ?
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