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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
Replies
0
votes
0
replies
33
views
Gene ontology with locus tags
ontology
locus
gene
tags
1 hour ago by
sea.joson
▴ 10
0
votes
1
reply
41
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 4 minutes ago by
andres.firrincieli
3.1k • written 2 hours ago by
harish
• 0
0
votes
6
replies
105
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 20 minutes ago by
GenoMax
125k • written 2 hours ago by
luzglongoria
▴ 40
0
votes
1
reply
105
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
updated 2 hours ago by
GenoMax
125k • written 6 hours ago by
ibq.enriquepola
• 0
0
votes
0
replies
56
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
8 hours ago by
manaswiniparija3
▴ 10
0
votes
0
replies
60
views
scATAC merging of files
Signac
scATAC-seq
12 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
74
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
14 hours ago by
anubratadas
▴ 20
0
votes
0
replies
91
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
14 hours ago by
bioinfo
▴ 20
0
votes
0
replies
78
views
Trimmomatic
RNA
check
quality
fastaq
Trimmomatic
14 hours ago by
Monia
• 0
0
votes
0
replies
81
views
VNTR genotyping
NGS
VNTR
genotyping
15 hours ago by
Genotepes
▴ 950
0
votes
0
replies
71
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
15 hours ago by
CH1374
▴ 10
0
votes
0
replies
71
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
16 hours ago by
a.bibek52
• 0
0
votes
0
replies
69
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
16 hours ago by
a.bibek52
• 0
2
votes
2
replies
149
views
Analyzing bulk RNA-seq
RNAseq
updated 15 hours ago by
swbarnes2
13k • written 17 hours ago by
Zaid
• 0
1
vote
13
replies
289
views
RNAseq for DE purpose
RNAseq
updated 15 hours ago by
swbarnes2
13k • written 18 hours ago by
m.habib
• 0
0
votes
0
replies
65
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase
off-target
SNPS
WGS
dCas9
19 hours ago by
pd378
• 0
0
votes
0
replies
60
views
SVA correction reduces ability to detect genes as differential expressed?
effects
RNAseq
expression
batch
SVA
gene
20 hours ago by
MB
▴ 50
0
votes
4
replies
212
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
3 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
84
views
Remove duplicates in multifasta, where entries are paired
bash
python
21 hours ago by
SaltedPork
▴ 170
1
vote
1
reply
104
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 18 hours ago by
Ram
37k • written 21 hours ago by
Aidand
• 0
0
votes
0
replies
63
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq
deseq2
ampliseq
ion-torrent
R
22 hours ago by
Fernando
• 0
0
votes
0
replies
72
views
Combining mRNA and total RNA studies
RNA-Seq
bulk
updated 18 hours ago by
Ram
37k • written 22 hours ago by
aksh
• 0
0
votes
0
replies
66
views
Twist Exome Sequencing Data: Palindromic Tandem Insertion-Deletion
NGS
Artefact
Twist
Sequencing
Exome
1 day ago by
TraPS-VarI
• 0
0
votes
0
replies
123
views
Bootstrap in PhyML
phyml
bootstrap
1 day ago by
Jimpix
▴ 10
0
votes
0
replies
107
views
Cibersort phenotpe file to create signature matrix
deconvolution
cibersort
file
phenotype
1 day ago by
ce810b57
• 0
0
votes
0
replies
118
views
Enrichment map in python/ Pathway network by using python
interaction.
enrichment
network
pathway
analysis
1 day ago by
sonsunjirachote
• 0
0
votes
1
reply
163
views
How to analysis genomes with orthologs?
ortholog
genome
annotation
updated 1 day ago by
GenoMax
125k • written 1 day ago by
沛煒
• 0
0
votes
0
replies
107
views
Does the falcon input CLR reads need corrected by Canu?
Genome
assemble
1 day ago by
leeunfeng
• 0
0
votes
0
replies
95
views
CUT&RUN H3K27me3 normalization with spike-in
deepTools
1 day ago by
mohansri1
• 0
0
votes
0
replies
107
views
How to identify nodes in a network with a higher degree and higher edge variance?
network
variance
WGCNA
igraph
updated 1 day ago by
ATpoint
68k • written 1 day ago by
adR
▴ 100
0
votes
2
replies
174
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 1 day ago by
LChart
1.8k • written 1 day ago by
optimistsso4co3
▴ 100
0
votes
3
replies
234
views
Change accession number to chromosome number in reference genome
fasta
chromosome
updated 18 hours ago by
Ram
37k • written 1 day ago by
Tsigabu
• 0
0
votes
0
replies
81
views
Median depth across samples from multi-sample VCF
DP
bcftools
1 day ago by
alex.blakes
• 0
0
votes
5
replies
227
views
Add Information to Protein Fasta Headers
protein
fasta
functional-annotation
header
1 day ago by
ahmadjoyyia
• 0
3
votes
2
replies
158
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 22 hours ago by
rpolicastro
11k • written 1 day ago by
janinubinu
• 0
0
votes
0
replies
82
views
count_matrix.csv generated by "prepDE.py3" script in Python3
Stringtie
RNA-seq
1 day ago by
Pegasus
▴ 40
0
votes
3
replies
255
views
biological vs. technical definition of "insert size"
grinder
simulated-reads
shotgun-sequencing
updated 1 day ago by
ATpoint
68k • written 1 day ago by
sovrappensiero
▴ 50
0
votes
0
replies
77
views
Haloplex HS - should you remove duplicates?
deduplicate
Haloplex
duplicates
1 day ago by
amy__
▴ 50
0
votes
0
replies
83
views
Interpreting SnpEff output plots
NGS
Annotation
SnpEff
WGS
WES
2 days ago by
Alireza
▴ 20
0
votes
0
replies
75
views
Using DANPOS2 to determine nucleosome positions
MNase-seq
DANPOS
ENCODE
bigwig
2 days ago by
elisheva
▴ 120
0
votes
0
replies
82
views
How to determine the receptor and binding site of a protein transcribed from a gene
gene
2 days ago by
yoser4
▴ 10
0
votes
3
replies
153
views
blast engine error empty blast query vector
error
alignment
Blast
updated 1 day ago by
pbioinf
▴ 30 • written 2 days ago by
Sowmya Pulapet
▴ 10
0
votes
0
replies
93
views
WGCNA Error in moduleEigengenes: setting key from pcagrey to pcagrey_
wgcna
2 days ago by
瀚
• 0
0
votes
0
replies
96
views
Exon 1 coverage of ADAMTS2 gene
WGS
Coverage
2 days ago by
ramya
• 0
0
votes
0
replies
111
views
bcftools error: bcftools could not parse pval threshold loidly
bcftools
mpileup
2 days ago by
mut.patricia
▴ 20
0
votes
0
replies
132
views
How to show the correlation between the expression of one gene and all the cell miRNAs expression levels?
expression
miRNA
correlation
2 days ago by
Zahra
▴ 90
0
votes
2
replies
166
views
No variants found ( have problem in the handbook)
bcftools
handbook
variation_calling
igv
2 days ago by
quanyu
• 0
0
votes
0
replies
125
views
Anti-CRISPR and Cas protein interactions
crispr
anti-crispr
proteins
updated 2 days ago by
GenoMax
125k • written 2 days ago by
Moein
• 0
0
votes
0
replies
126
views
issues with amber_minimize.py failing to use CUDA within alphafold
linux
CUDA
amber
alphafold
2 days ago by
charlieclark1ee
▴ 10
1
vote
1
reply
154
views
tools that align sequences in mouse and human
r
updated 2 days ago by
dthorbur
▴ 260 • written 2 days ago by
Chironex
▴ 40
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Comment: RNAseq for DE purpose
Answer: High downstream gene expression
Answer: High downstream gene expression
Answer: High downstream gene expression
Answer: 'SyntaxError': 'return' outside function?
Comment: Analyzing bulk RNA-seq
The Biostar Handbook. A bioinformatics e-book for beginners.
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Comment: Clustering and dynamic tree cutting
by
andres.firrincieli
3.1k
> it produces 160 clusters. This is happening because the input is a simple correlation matrix that is affected by spurious or missing co…
Answer: When you convert a BAM back into a FastQ do you get the original Fastq?
by
GenoMax
125k
If the aligner writes reads that do not align by default to output (or you as the user chooses the right option for aligner to do so) then …
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
Memory =/= disk storage. Likely you will need to diagnose this yourself since we don't have access to your data/server. Your command obvio…
Comment: STAR is running but .sam file size does not increase after hours mapping
by
luzglongoria
▴ 40
Thanks for your reply. It is not a problem of memory since I can run other mapping analyses with no problem (I get big Sam output files w…
Comment: Translating gene names to entrez id's
by
GenoMax
125k
https://www.biostars.org/u/123097/ : Please post this as a new question. It is not directly related to this thread. Once you do that you ca…
Comment: Translating gene names to entrez id's
by
eliska.ochodkova
• 0
Dear all, I want to use the GoSim package to calculate the IC similarity. I'm trying to set the parameters of setEvidenceLevel(), but wr…
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
Is this a server administered by a sys admin? Do you know if individual user accounts have "quota"? If your user account has a storage qu…
Comment: STAR is running but .sam file size does not increase after hours mapping
by
luzglongoria
▴ 40
If I do df -h then I get Filesystem Size Used Avail Use% Mounted on devtmpfs …
Comment: RNASeq differential expression masked by pathways disregulation
by
i.sudbery
16k
It you really do have a reason to suspect that the biology of samples from CC1 is different from the biology of samples from CC2, and that …
Answer: High downstream gene expression
by
i.sudbery
16k
You don't show which species this is. I've taken a quick look at the human and mouse genome at those locations and neither have any genes a…
Comment: Annotating ENS codes to gene name
by
GenoMax
125k
This is a FAQ, Some past threads linked here: https://www.biostars.org/p/9552097/#9552101
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
You are not running out of storage quota on the particular disk?
Comment: STAR is running but .sam file size does not increase after hours mapping
by
luzglongoria
▴ 40
I have tried reducing the number of threads but it is the same.
Answer: High downstream gene expression
by
Matthias Zepper
2.9k
1. Impossible to tell from the information you are showing. Could be misalignments, [read-through transcription][1] ([detection pipeline][…
Answer: Annotating ENS codes to gene name
by
Apex92
▴ 240
You can either use biomart to download all gene ids and gene names and then intersect them with your current table. Or you can use your ann…
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