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110,504 results • Page
1 of 2211
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Votes
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0
votes
0
replies
5
views
Is PanCan data microarray or rna-seq
pancan
rna
rna-seq
microarray
data
10 minutes ago by
survive
• 0
0
votes
1
reply
20
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 40 minutes ago by
seidel
11k • written 1 hour ago by
dare_devil
★ 3.1k
0
votes
1
reply
113
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
1 hour ago by
Apprentice
▴ 140
6
votes
8
replies
561
views
Help with running ATAC using Encode pipeline
encode
ATAC-seq
40 minutes ago by
Chris
▴ 100
0
votes
2
replies
2.8k
views
How to run Picard docker image
next-gen
alignment
docker
picard
updated 6 hours ago by
geocarvalho
▴ 330 • written 3.7 years ago by
elcortegano
▴ 180
744
votes
162
replies
114k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
0
votes
0
replies
58
views
Job:
Associate Professor, Ecology
Ecology
updated 7 hours ago by
Ram
39k • written 8 hours ago by
jterakita
▴ 20
0
votes
2
replies
85
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
just now by
JACKY
▴ 100
0
votes
0
replies
51
views
CIBERSORT Error: File not found
CIBERSORT
9 hours ago by
jcara514
• 0
3
votes
3
replies
170
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 2 hours ago by
rfran010
▴ 160 • written 11 hours ago by
shamza
• 0
0
votes
2
replies
214
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 12 hours ago by
Ram
39k • written 1 day ago by
B.N.
• 0
0
votes
3
replies
194
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 7 hours ago by
Ram
39k • written 13 hours ago by
Researcher
• 0
7
votes
6
replies
295
views
Contigs to chromosomes annotation
Assembly
mapping
contigs
updated 12 hours ago by
GenoMax
129k • written 1 day ago by
alexandru.bologa.marian
▴ 50
2
votes
3
replies
196
views
Gene prediction software
pseudogene
gene
prediction
masking
10 minutes ago by
subashini.fbtpb106
▴ 10
1
vote
6
replies
262
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
4 hours ago by
melissachua90
▴ 40
1
vote
0
replies
85
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
16 hours ago by
zhangdengwei
▴ 190
0
votes
1
reply
110
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
updated 10 hours ago by
acvill
▴ 290 • written 17 hours ago by
tahsinkhan570
• 0
2
votes
3
replies
204
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 15 hours ago by
GenoMax
129k • written 17 hours ago by
ev97
• 0
0
votes
0
replies
96
views
Which is the minor allele in ped file in plink?
plink
updated 18 hours ago by
GenoMax
129k • written 18 hours ago by
khn
▴ 130
0
votes
2
replies
170
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
8 hours ago by
mattze731
▴ 10
1
vote
1
reply
236
views
Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
16S
dada2
DECIPHER
ITS
taxonomy
19 hours ago by
mattze731
▴ 10
0
votes
0
replies
91
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
20 hours ago by
F.Bedjou
▴ 10
0
votes
0
replies
86
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
20 hours ago by
Coremine Medical
▴ 10
2
votes
1
reply
140
views
Visualizing Graph Alignment Format via minigraph
graph
gaf
minigraph
alignment
updated 21 hours ago by
colindaven
4.9k • written 1 day ago by
ivazirabad
▴ 20
0
votes
2
replies
222
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 20 hours ago by
ATpoint
72k • written 4 days ago by
fr
▴ 200
1
vote
2
replies
238
views
What kind of statistical test does Cellranger count use?
scRNAseq
10X
Single-Cell
updated 22 hours ago by
fracarb8
▴ 950 • written 1 day ago by
hannah
• 0
3
votes
7
replies
4.1k
views
Getting Pairwise Sequence Alignment Score With Biopython
biopython
alignment
clustalw
updated 19 hours ago by
Jonathan Lefebre
▴ 70 • written 11.5 years ago by
Lakshmi
• 0
0
votes
0
replies
75
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
23 hours ago by
hashim.rana11
▴ 20
2
votes
4
replies
247
views
Get relationships and hierarchies for GO terms
GO-terms
Gene-onthology
updated 21 hours ago by
Alexander
▴ 70 • written 1 day ago by
DanielEB_fisk
▴ 10
0
votes
0
replies
105
views
Integrate RDS files
integration
1 day ago by
Andy
▴ 50
6
votes
17
replies
4.5k
views
8 follow
Eigen genes using WGCNA
wgcna
eigengenes
updated 1 day ago by
chaco001
▴ 40 • written 4.7 years ago by
shivangi.agarwal800
▴ 120
7
votes
6
replies
288
views
Italicise annotations with pheatmap
R
Pheatmap
updated 23 hours ago by
ATpoint
72k • written 1 day ago by
jamie.pike
▴ 80
1
vote
3
replies
407
views
NanoSim Error "Please specify the training reads and its reference genome!"
NanoSim
RNA-seq
LongRead
1 day ago by
akainth
▴ 10
0
votes
1
reply
144
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 1 day ago by
Ram
39k • written 1 day ago by
akainth
▴ 10
0
votes
8
replies
5.9k
views
Bedtools problem : It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited
bedtools
fasta
updated 1 day ago by
Michael
• 0 • written 3.6 years ago by
Tomm
• 0
0
votes
4
replies
1.7k
views
Spatial transcriptomics without the h5 file
h5
spatial-transcriptomics
updated 1 day ago by
Ram
39k • written 17 months ago by
jordi.diaz-manera
▴ 10
1
vote
9
replies
309
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 1 day ago by
Ram
39k • written 1 day ago by
peavy
• 0
2
votes
2
replies
236
views
Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
Dendrogram
R
Heatmap
ComplexHeatmap
updated 1 day ago by
jv
★ 1.2k • written 2 days ago by
Manuel
• 0
0
votes
1
reply
374
views
How to quantification proteomics data
proteomics
updated 1 day ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
4
replies
215
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
1 day ago by
Daniel
▴ 30
0
votes
2
replies
1.4k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 1 day ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
0
replies
96
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
1 day ago by
eqoa45
• 0
3
votes
3
replies
320
views
Perl. How to retrieve data until a keyword in GenBank?
fasta
sequence
GenBank
perl
1 day ago by
Fungi-Beware!
▴ 10
0
votes
1
reply
159
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
updated 1 day ago by
jared.andrews07
★ 14k • written 1 day ago by
B.N.
• 0
1
vote
0
replies
104
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
1 day ago by
Dan
▴ 120
6
votes
7
replies
341
views
NCBI API, Perl
API
NCBI
updated 1 day ago by
GenoMax
129k • written 1 day ago by
alessandro.alma00
• 0
1
vote
2
replies
168
views
hisat2 Error 137
hisat2
RNA-seq
1 day ago by
Forough
▴ 10
0
votes
0
replies
104
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
1 day ago by
xeod21
• 0
1
vote
0
replies
125
views
Herald:
The Biostar Herald for Monday, June 05, 2023
herald
1 day ago by
Biostar
1.8k
2
votes
1
reply
143
views
Is RNA-Seq well suited for studying pseudogenes and lncRNA?
rna
ncRNA
transcriptome
pseudogene
rna-seq
updated 1 day ago by
rpolicastro
12k • written 1 day ago by
Kermit
▴ 80
110,504 results • Page
1 of 2211
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bcl2fastq2: how to correctly use the --use-bases-mask for different sequencing methods by Illumina ?
Answer: How to calculate TPM from featureCounts output
Answer: How to calculate TPM from featureCounts output
Comment: How to calculate TPM from featureCounts output
Comment: Asking for feedback on a Python library for computing alignments
Comment: Asking for feedback on a Python library for computing alignments
Comment: Asking for feedback on a Python library for computing alignments
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Comment: Gene prediction software
by
subashini.fbtpb106
▴ 10
Thanks for the answer. The draft genome of walking catfish Clarias magur with the coverage of 94 percent of estimated genome size. Assembl…
Comment: How to calculate TPM from featureCounts output
by
survive
• 0
featureCounts file
Comment: Help with running ATAC using Encode pipeline
by
Chris
▴ 100
Yes, I think that is what the pipeline wants. I didn't see tutorials or videos which are easy to follow for new users so just reading the i…
Comment: What is the possibility of Depth (DP) being higher than the coverage
by
seidel
11k
100x coverage is an average for the exome. Individual loci will vary. Did you try calculating the coverage yourself to see how it varies? O…
Answer: PRSice-2 using SNPs with extremely low P-value
by
Apprentice
▴ 140
I had asked the same question on PRSice's git hub. I got an answer from the developer and will share it here as well. https://github.com/c…
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴ 160
> I am not sure what to put in the input file. Is it something like > this? What input file are you referring to? Your fastqs are given in…
Comment: retaining only the clusters of interest
by
rfran010
▴ 160
I usually use select to choose which columns to keep, but not sure if this subset function is specific to seurat ( I am completely unfamili…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I added the dput. Thanks for the reminder!
Comment: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
Please show the design matrix or the code used to create the design matrix. The result you report is a common occurrence when people mista…
Comment: What does "OS_CNSR" and "PFS_CNSR" mean?
by
GenoMax
129k
[**From this doc**][1]: **CNSR** variable is created based on the event occurrence and the values are 0 (when the event occurs) and 1 (comp…
Answer: How to run Picard docker image
by
geocarvalho
▴ 330
I had the same issue, but I found out in the previous GitHub issues that it was made in a way to run like this: ```bash docker run broadins…
Comment: calculate p value and associated z score for snp-gene pair
by
rheab1230
▴ 140
Thank you so much for the information.
Comment: Gviz Coverage Plots
by
Ram
39k
I understand that but stick to one place at least for a while and always link to other places you've posted (reasonable places, we don't ne…
Comment: Gviz Coverage Plots
by
Researcher
• 0
Sorry, I didn't know that posting it on another forum was rude but I really need help with this.
Comment: Correct way to remove Nextera adapters from ITS sequences
by
mattze731
▴ 10
Trimmomatic allows to enter custom adapter sequences, but I don't see how this would change the outcome. Similarly, trimmomatic also allows…
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