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54 results • Page
1 of 2
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1
vote
13
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289
views
RNAseq for DE purpose
RNAseq
updated 14 hours ago by
swbarnes2
13k • written 18 hours ago by
m.habib
• 0
7
votes
8
replies
1.6k
views
How can we time a recent gene duplication event using (neutral?) DNA mutations as molecular clock?
molecular-clock
gene-duplication
phylogeny
updated 14 hours ago by
Ram
37k • written 7.7 years ago by
xiaofeng.dong12
▴ 20
1
vote
6
replies
2.0k
views
Error using samtools for downloading bam files
bam
samtools
updated 17 hours ago by
Ram
37k • written 7.7 years ago by
Maria333
▴ 20
0
votes
5
replies
558
views
Create phylogenetic tree of 144 species
phylogenetic-tree
updated 17 hours ago by
Ram
37k • written 5 weeks ago by
anasjamshed1994
▴ 120
0
votes
5
replies
2.2k
views
CEGMA on human assembly
CEGMA
Assembly
updated 15 hours ago by
Ram
37k • written 7.7 years ago by
ulike
• 0
0
votes
5
replies
2.8k
views
Graph using corrplot for multiple sets of data
R
updated 15 hours ago by
Ram
37k • written 7.7 years ago by
rvsaras86
• 0
7
votes
4
replies
1.3k
views
microarray gene datasets
gene
updated 18 hours ago by
Ram
37k • written 7.7 years ago by
bioinfo
▴ 60
0
votes
4
replies
208
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
2 hours ago by
bioinformatics.girl
• 0
0
votes
4
replies
262
views
Help converting .CYCHP to .txt or .csv or .vcf
cychp
20 hours ago by
Sarah
• 0
0
votes
4
replies
70
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 22 minutes ago by
GenoMax
125k • written 2 hours ago by
luzglongoria
▴ 40
2
votes
3
replies
457
views
samtools mpileup error - 1 samples in 1 input files
samtools
bioinformatics
SAM
BAM
mpileup
updated 20 hours ago by
Pierre Lindenbaum
152k • written 13 months ago by
joseph.kelly.94
▴ 10
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
3
replies
206
views
bwa-meth unrecognized reference name during sam_parse
EM-seq
Methyl-seq
alignment
bwa-meth
updated 21 hours ago by
GenoMax
125k • written 6 days ago by
bp22
▴ 20
0
votes
3
replies
465
views
Merging compressed fastq files based on a conditions defined in a csv file
bash
linux
updated 16 hours ago by
Ram
37k • written 12 months ago by
D
• 0
3
votes
2
replies
158
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 21 hours ago by
rpolicastro
11k • written 1 day ago by
janinubinu
• 0
2
votes
2
replies
149
views
Analyzing bulk RNA-seq
RNAseq
updated 14 hours ago by
swbarnes2
13k • written 17 hours ago by
Zaid
• 0
0
votes
1
reply
2.2k
views
missing probeID in affymetrix using oligo package
affymetrix
updated 17 hours ago by
Ram
37k • written 7.7 years ago by
benhrif.oussama
• 0
0
votes
1
reply
277
views
How to calculate 2.5% pvalues for the 2 ends of the distribution?
numpy
t-test
python
genomics
updated 17 hours ago by
Ram
37k • written 6 weeks ago by
Virat_Baahubali
• 0
0
votes
1
reply
1.8k
views
Comparison of two structures based on only partial similarly (comparison of cores of proteins/rna)
protein
structural-comparison
rna
updated 16 hours ago by
Ram
37k • written 7.8 years ago by
mmagnus
▴ 150
0
votes
1
reply
102
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
updated 1 hour ago by
GenoMax
125k • written 6 hours ago by
ibq.enriquepola
• 0
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
1
reply
348
views
How can I find high copy number sequence in Bacteria genome?
Bacteria
updated 16 hours ago by
Ram
37k • written 11 months ago by
amirsangi2628
• 0
0
votes
1
reply
285
views
Finding AIC using R for best DNA models and open MSA on web browser on given multisequence fasta file.
msa
R
updated 16 hours ago by
Ram
37k • written 11 months ago by
Platelet Guardian
• 0
0
votes
1
reply
390
views
sorting clusters from cd hit
cd-hit
updated 17 hours ago by
Ram
37k • written 5 weeks ago by
Nabil
• 0
0
votes
1
reply
162
views
Identifying whether a sequence is Novel or not
Novel-sequence
WGS
updated 17 hours ago by
Ram
37k • written 11 days ago by
Mustafa
• 0
0
votes
1
reply
1.4k
views
issues in genotyping using TaqMan Assay
TaqMan
genotyping
updated 15 hours ago by
Ram
37k • written 7.7 years ago by
jfjiang
▴ 10
1
vote
1
reply
340
views
Getting a PhD in Bioinformatics only having a BSc in Data Science
software-development
project
updated 16 hours ago by
Ram
37k • written 12 months ago by
d
• 0
1
vote
1
reply
271
views
How do I subset a dataframe based on several other dataframes using R?
R
affymetrix
updated 16 hours ago by
Ram
37k • written 12 months ago by
melissachua90
▴ 40
0
votes
0
replies
28
views
Gene ontology with locus tags
ontology
locus
gene
tags
1 hour ago by
sea.joson
▴ 10
0
votes
0
replies
69
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
15 hours ago by
a.bibek52
• 0
0
votes
0
replies
84
views
Remove duplicates in multifasta, where entries are paired
bash
python
20 hours ago by
SaltedPork
▴ 170
0
votes
0
replies
60
views
SVA correction reduces ability to detect genes as differential expressed?
effects
RNAseq
expression
batch
SVA
gene
19 hours ago by
MB
▴ 50
0
votes
0
replies
190
views
Comparative genomic analysis for domestication related traits
genomics
updated 17 hours ago by
Ram
37k • written 4 weeks ago by
shwetamgr1
▴ 10
2
votes
0
replies
195
views
Should one concatenate two haplotype genome assemblies into one assembly?
PacBio
genome-assembly
whole-genome-sequence
Hi-C
updated 16 hours ago by
Ram
37k • written 11 months ago by
anikcropscience
▴ 150
0
votes
0
replies
73
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
13 hours ago by
anubratadas
▴ 20
0
votes
0
replies
1.4k
views
Using GWAS data to reproduce the gene candidate results
snp
updated 17 hours ago by
Ram
37k • written 7.7 years ago by
huudaudi
• 0
0
votes
0
replies
78
views
Trimmomatic
RNA
check
quality
fastaq
Trimmomatic
13 hours ago by
Monia
• 0
0
votes
0
replies
2.7k
views
CNV analysis from SNP6.0 data using Affymetrix power tools
cnv
apt-copynumber
SNP
affymetrix
updated 15 hours ago by
Ram
37k • written 7.7 years ago by
cafelumiere12
▴ 80
0
votes
0
replies
129
views
Normalizing expression values
normalization
Scanpy
logCPM
scRNA
updated 17 hours ago by
Ram
37k • written 5 days ago by
mt_pereira
• 0
0
votes
0
replies
198
views
Comparing mapped reads between long-read bulk RNA-seq samples
transcriptomics
RNA-seq
TPM
long-read
updated 17 hours ago by
Ram
37k • written 6 weeks ago by
ghs101
• 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
81
views
VNTR genotyping
NGS
VNTR
genotyping
14 hours ago by
Genotepes
▴ 950
0
votes
0
replies
2.2k
views
Coverage and Read Depth Recommendations by Sequencing Application
coverage
sequencing-depth
updated 15 hours ago by
Ram
37k • written 7.7 years ago by
support
▴ 640
0
votes
0
replies
65
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase
off-target
SNPS
WGS
dCas9
18 hours ago by
pd378
• 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
23 hours ago by
TraPS-VarI
• 0
0
votes
0
replies
90
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
13 hours ago by
bioinfo
▴ 20
0
votes
0
replies
35
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
1 hour ago by
harish
• 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
71
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
15 hours ago by
CH1374
▴ 10
54 results • Page
1 of 2
Recent Votes
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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Recent Replies
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…
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
• 0
This does not work. I called for the gene "Cd8a" for instance for the mouse genome and it says "Gene not found" even though it should appea…
Comment: How to extract the list of genes from TCGA CNV data
by
Kevin Blighe
84k
Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
Comment: RNASeq differential expression masked by pathways disregulation
by
ATpoint
68k
If this is the case then you cannot correct for anything as this effect is nested with center.
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
That error message is very descriptive. Could you also add the line 997531?
Comment: RNASeq differential expression masked by pathways disregulation
by
Gama313
▴ 110
Thanks for the answer. However I am not sure this could be considered batch since CC2 samples have true upregulation of specific pathways t…
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