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90,538 results • Page
1 of 1811
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Votes
Replies
0
votes
0
replies
9
views
Installing perl modules on a conda environment produce changes out of the environment?
conda
perl
2 hours ago by
v.berriosfarias
▴ 10
0
votes
0
replies
26
views
Codon alignment with degenerate nucleotides?
paml
codeml
codon
alignment
3 hours ago by
DNAlias
▴ 10
583
votes
155
replies
64k
views
89 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
tutorial
training
News
updated 8 days ago by
Biostar
10 • written 4.4 years ago by
Istvan Albert
87k
1
vote
1
reply
45
views
Make New Orig.ident in seurat object or
R
RNA-SEQ
Seurat
updated 7 hours ago by
fracarb8
▴ 140 • written 8 hours ago by
Maria17
• 0
0
votes
1
reply
71
views
RNAseq
gffcompare
error
stringtie
rnaseq
updated 6 hours ago by
Kevin Blighe
72k • written 9 hours ago by
mtavakoli4030
• 0
1
vote
2
replies
74
views
Duplicated Gene Symbol names after geneID conversion
geneID
updated 8 hours ago by
GenoMax
99k • written 9 hours ago by
asumani
▴ 70
1
vote
1
reply
60
views
How to merge two GTFs which share some common features
stringtie
GTF
annotation
9 hours ago by
emalekos
• 0
0
votes
0
replies
37
views
my gffcompare out put gtf file is like that. on complete row is followed by some uncomplete row wich have not class codes.
gffcompare
rna
lncrna
gtf
updated 13 hours ago by
GenoMax
99k • written 15 hours ago by
mtavakoli4030
• 0
0
votes
0
replies
41
views
Skewed Betweenness Centrality values resulting in almost unusable PPI networks for my university project - what can I do?
Bioinformatics
Cytoscape
16 hours ago by
gemmalouisebaldock
▴ 20
1
vote
1
reply
78
views
Performance metrics of aligners and variant callers
benchmarking
WGS
updated 15 hours ago by
Jeremy Leipzig
20k • written 20 hours ago by
Prashant
▴ 10
2
votes
2
replies
133
views
News:
Bioinformatics Solutions on AWS
AWS
Bioinformatics
Cloud
15 hours ago by
Jillian
▴ 20
6
votes
11
replies
353
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq
DESeq2
just now by
sumitguptabt
▴ 10
0
votes
1
reply
61
views
making a PCA from MASH distance result
MASH
R
PCA
updated 21 hours ago by
5heikki
9.7k • written 22 hours ago by
v.berriosfarias
▴ 10
0
votes
0
replies
44
views
Query on miRDeep2
mirDeep2
mapper
updated 20 hours ago by
Gjain
5.6k • written 1 day ago by
mithu18mohan
• 0
3
votes
2
replies
155
views
Negative values in Cox regression analysis
survival
CoxPH
coxregression
1 day ago by
Mran
▴ 20
2
votes
1
reply
123
views
Bam file metrics
ngs
bam
gatk
updated 1 day ago by
GenoMax
99k • written 1 day ago by
Sabeen
• 0
0
votes
2
replies
170
views
bedtool closest
bedtool
updated 9 hours ago by
Ram
32k • written 1 day ago by
CHINMAYA
• 0
2
votes
3
replies
216
views
Visualize DNA sequence as a dot plot?
plot
visualization
DNA
dot
updated 1 day ago by
Alex Reynolds
32k • written 5 days ago by
jaydu
• 0
0
votes
0
replies
67
views
How should we replace NAs from a genelight object?
R
glpca
adegenet
GBS
SNP
1 day ago by
jaafari.omid
▴ 50
1
vote
2
replies
108
views
To create amino acid substitution in protein structure
protein
bioinformatics
software
20 hours ago by
shwetamgr1
• 0
0
votes
1
reply
72
views
Protein-Protein interaction for Upregulated genes
STRING
DEGs
PPI
updated 1 day ago by
Mensur Dlakic
★ 10k • written 1 day ago by
1961012
• 0
0
votes
2
replies
88
views
Geno Ontology Analysis
GO
hypergtest
updated 1 day ago by
h.mon
32k • written 1 day ago by
1961012
• 0
1
vote
3
replies
206
views
How to retrieve protein sequence from gene ID and output a fasta file
ncbi
gene
protein
biopython
entrez
updated 1 day ago by
GenoMax
99k • written 2 days ago by
minifoog
• 0
0
votes
0
replies
42
views
drug resistance informations for variations
cosmic
somatic
drug
variants
germline
1 day ago by
enes
• 0
0
votes
1
reply
62
views
DiffBind consensus peak extraction
DiffBind
ChIP-seq
updated 1 day ago by
Rory Stark
★ 1.0k • written 1 day ago by
wei.zhang
• 0
1
vote
2
replies
79
views
hisat2 output from paired en reads.
hisat2
rna-seq
updated 1 day ago by
Zhilong Jia
★ 1.7k • written 1 day ago by
Palgrave
▴ 30
1
vote
2
replies
90
views
GATK variant annotation
vcf
gatk
updated 1 day ago by
Ram
32k • written 1 day ago by
shubhamkumbhar420
• 0
0
votes
0
replies
48
views
Assembly pipeline for SMRT (PacBio) sequenced bacterial genome data?
sequence
genome
perl
python
pipeline
1 day ago by
Kumar
▴ 50
0
votes
0
replies
32
views
MACS2 Summit TSSPlot dividing BDG into bins
TSS
Callpeaks
MACS2
1 day ago by
Seigfried
▴ 70
0
votes
0
replies
1.8k
views
Include - in part of the motif for analysis? And "It looks like we don't support this file format" when opening weblogo motif
motif
aminoacids
sequence
biopython
weblogo
1 day ago by
minifoog
• 0
0
votes
0
replies
86
views
LD score regression of data including SNPs with extremely low P-value
heritability
SNP
LDSC
1 day ago by
Apprentice
▴ 50
0
votes
1
reply
108
views
gRNA concatamer - will it work ?
gRNA
CRISPR
PAM
updated 1 day ago by
ATpoint
48k • written 2 days ago by
Rajesh
• 0
3
votes
1
reply
76
views
Understanding the ColData Matrix
RNA-SEQ
R
Micheal_Love
DESEQ2
updated 2 days ago by
jared.andrews07
9.3k • written 2 days ago by
raisamathenge
▴ 30
0
votes
0
replies
120
views
Job:
Bioinformatician/Programmer at the University of Pennsylvania
pipelines
programmer
bioinformatician
python
r
2 days ago by
adamnaj
• 0
0
votes
0
replies
70
views
Job:
Bioinformatician at Turbine / Hungary
proteomics
cancerreserach
singlecell
python
r
2 days ago by
timea.volenter
• 0
0
votes
0
replies
44
views
panel of normals for mutect2
mutect2
gatk
NGS
PoN
somatic
2 days ago by
lait
▴ 160
0
votes
2
replies
101
views
format conversion using OpenBabel
software
1 day ago by
roybatty269
• 0
0
votes
0
replies
54
views
How to compare enrichment scores?
enrichment
scores
2 days ago by
fpizzagalli
• 0
0
votes
0
replies
46
views
Should I take FDR < 0.2 for differentially abundant bacteria found in meta-analysis random effect ?
FDR
Microbiome
2 days ago by
deep771992chanda
▴ 30
0
votes
1
reply
79
views
Program for predicting RNA sequences that may bind to a protein Domain
protein
Binding
domain
RNA
updated 2 days ago by
Mensur Dlakic
★ 10k • written 2 days ago by
noahhelton98
▴ 10
2
votes
5
replies
271
views
Understanding TCGA's ASCAT copy number data
tcga
ascat
copy number
updated 2 days ago by
Zhenyu Zhang
▴ 280 • written 6 weeks ago by
loughrae
▴ 70
0
votes
1
reply
120
views
GDC Data Query
RNA-Seq
updated 2 days ago by
Zhenyu Zhang
▴ 280 • written 4 weeks ago by
p20170409
• 0
1
vote
3
replies
103
views
Redundancy reduction of de novo transcriptome assemblies with Compacta?
de-novo
transcriptome
redundancy-reduction
1 day ago by
Dunois
▴ 630
0
votes
5
replies
154
views
Cellranger count.srun issues
cellranger
srun
updated 2 days ago by
GenoMax
99k • written 2 days ago by
gonzalezb549
• 0
1
vote
2
replies
119
views
Up-to-date GWAS Power Calculator and GWAS power comparison
GWAS
power
6 hours ago by
moxu
▴ 480
1
vote
1
reply
2.3k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA
RNA-seq
updated 2 days ago by
Kevin Blighe
72k • written 4 days ago by
leesooyeon94
▴ 10
3
votes
2
replies
162
views
Contradiction in Harzard ratio and Log fold change
Foldchange
Cancer
HR
HarzardRatio
LogFC
1 day ago by
Mran
▴ 20
0
votes
0
replies
48
views
Refs/tools for protein interactomes
Protein
PSI-MI
Interactome
Orthologs
PPI
2 days ago by
ian.will
• 0
0
votes
4
replies
162
views
How to plot a image like this.
plot
Bioinformatics
Cancer
R
Genome
2 days ago by
lincaijin1994
• 0
1
vote
2
replies
131
views
HaplotypeCaller VCF depth is greater than the number of reads in bam
HaplotypeCaller
vcf
gatk
2 days ago by
wang.yiguan
• 0
90,538 results • Page
1 of 1811
Recent Votes
Comment: RNAseq data analysis of pooled data
Answer: RNAseq data analysis of pooled data
Normalisation of read mapping counts to account for contig length
Answer: Limiting variant calls to amplicon target regions?
Converting TCGA expression data from FPKM to TPM
C: Raw counts to TPM in R
Answer: Duplicated Gene Symbol names after geneID conversion
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Recent Replies
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a
by
sumitguptabt
▴ 10
Dear, please help me, I am new in this field. Please tell me if it is the right way or needs some correction.
Comment: RNAseq
by
Kevin Blighe
72k
Hi, can you please choose a more informative question title? Also, can you take a look at how I use `gffread`, here: https://www.biostars.…
Comment: Up-to-date GWAS Power Calculator and GWAS power comparison
by
moxu
▴ 480
Hi Kevin, Thanks for the reply. I had checked out CaTS before posting above. However, I am not sure if CaTS does what I want to do. Suppo…
Comment: Arlequin problem (different loci number among different genotypes)
by
wangh920
• 0
For sure, The reason why this happen is because SNP calling generate a couple of biallelic SNP, such as GC, GT or GCT, GCG. These allelic…
Answer: Make New Orig.ident in seurat object or
by
fracarb8
▴ 140
You can use `strsplit` to extract the first entry before the `_` metadata <- seurat_object@meta.data metadata$orig.ident <- …
Comment: How to solve the problem when I get error message "column 1 is not a genotype ob
by
Bornali
• 0
Hi Devon Ryan. I am trying to add genotype object to my SNP data set. I am unable to use the codes described in the subsequent comment as m…
Comment: Duplicated Gene Symbol names after geneID conversion
by
asumani
▴ 70
opss, didn't notice that thread. many thanks!
Answer: Duplicated Gene Symbol names after geneID conversion
by
GenoMax
99k
See: https://www.biostars.org/p/352492/#352535
Comment: Can't count features with featurecount
by
avelarbio46
▴ 10
After using these options, I got decreased aligment in general than with "-F GTF -s 0 -p -T 8 -a ". I have not tried with -M and -O on 1 or…
Comment: How to merge two GTFs which share some common features
by
GenoMax
99k
See the answers and discussion in: https://www.biostars.org/p/9465577/
Comment: single tumor vs multiple normal sample differential gene expression (RNA-Seq ) a
by
sumitguptabt
▴ 10
Dear @atpoint Thank you so much for your help, I can not describe my happiness. I run your script and got the output as you see in the att…
Comment: How to run SPAdes assembler with bam files?
by
GenoMax
99k
Sorted files compress better so the size being smaller is not a particular surprise. Have you checked to see that you are getting reads at …
Comment: How to run SPAdes assembler with bam files?
by
marongiu.luigi
▴ 560
Thank you. Actually I am getting an unmapped.bam file of 132 Mb, a sorted version of 34 Mb (shouldn't they be the same weight) and fastq of…
Comment: Bioinformatics Solutions on AWS
by
Jillian
▴ 20
I had that pointed out to me, but thanks for the heads up! I know it's a problem. I wrote the book using Sphinx, and I have to figure out h…
Comment: Performance metrics of aligners and variant callers
by
Devon Ryan
98k
Have you searched pubmed? By now there must be hundreds of papers that do this. Just read a few if you're uncertain which tools might work …
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