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120,879 results • Page
1 of 2418
Sort: Rank
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0
votes
0
replies
4
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
just now by
harsh
• 0
0
votes
0
replies
18
views
boxplot wilcox test
R
boxplot
34 minutes ago by
pinheirofabiano
▴ 100
0
votes
1
reply
86
views
MULTIQC for miRNAseq data
multiqc
updated 3 hours ago by
i.sudbery
21k • written 17 hours ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
85
views
How to improve the mapping rate of vg giraffe
vg
updated 3 hours ago by
colindaven
7.3k • written 11 hours ago by
gulin
• 0
0
votes
5
replies
121
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
updated 1 hour ago by
GenoMax
150k • written 5 hours ago by
paulanavarrete116
• 0
2
votes
3
replies
156
views
Issues with vg surject into paths
vg
updated 3 hours ago by
GenoMax
150k • written 1 day ago by
Rugare
• 0
835
votes
169
replies
172k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
63
views
Missing short indels from vcf
bcftools
shortindels
mpileup
14 hours ago by
kbranger
• 0
8
votes
12
replies
289
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 5 hours ago by
LauferVA
4.6k • written 20 hours ago by
ka132
▴ 10
0
votes
3
replies
118
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 15 hours ago by
GenoMax
150k • written 17 hours ago by
bge
• 0
0
votes
1
reply
89
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 15 hours ago by
GenoMax
150k • written 15 hours ago by
shpak.max
▴ 50
0
votes
2
replies
109
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
1 hour ago by
Diego
▴ 110
1
vote
1
reply
74
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 15 hours ago by
GenoMax
150k • written 16 hours ago by
ParastooA
▴ 20
0
votes
1
reply
71
views
Checking sex of a sample with sequencing data
ATAC-seq
updated 1 hour ago by
ATpoint
87k • written 16 hours ago by
xqyn
▴ 30
0
votes
5
replies
303
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 21 hours ago by
Istvan Albert
102k • written 2 days ago by
shu8
• 0
1
vote
1
reply
94
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 21 hours ago by
i.sudbery
21k • written 21 hours ago by
ATS
• 0
0
votes
2
replies
132
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
updated 19 hours ago by
GenoMax
150k • written 23 hours ago by
dk7258859
• 0
0
votes
1
reply
201
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 22 hours ago by
lieven.sterck
15k • written 3 days ago by
Jl
• 0
1
vote
3
replies
135
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 1 day ago by
GenoMax
150k • written 1 day ago by
Ana
• 0
0
votes
1
reply
100
views
cant make the correct matrix
logfc
csv
updated 1 day ago by
lieven.sterck
15k • written 1 day ago by
Naila
• 0
1
vote
4
replies
143
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
23 hours ago by
SomeOne
▴ 170
1
vote
7
replies
211
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 1 day ago by
yura.grabovska
▴ 750 • written 1 day ago by
zhang616123
• 0
0
votes
3
replies
152
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
updated 6 hours ago by
Bastien Hervé
6.2k • written 1 day ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
75
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
1 day ago by
soledad.esteban
• 0
0
votes
4
replies
153
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 1 day ago by
ATpoint
87k • written 1 day ago by
ZuelTech
• 0
1
vote
14
replies
439
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 1 day ago by
colindaven
7.3k • written 2 days ago by
ZuelTech
• 0
1
vote
4
replies
965
views
Should I process two complete sets of 10x single-cell multiomics sequencing files from one donor together or separately?
10x_multiome
ENCODE
cellranger_arc
updated 1 day ago by
swbarnes2
14k • written 3 days ago by
Wu-Sheng Zhang
• 0
1
vote
4
replies
218
views
Count matrices plotting
count
matrix
scanpy
1 day ago by
NIkita
• 0
3
votes
8
replies
248
views
Filter snRNA-seq .fastq files based on barcodes
snRNA-seq
scRNA-seq
FASTQ
bbmap
updated 17 hours ago by
GenoMax
150k • written 1 day ago by
connorjfausto
▴ 30
0
votes
1
reply
142
views
Defining Sex Chromosomes in PLINK for a Camel Genome
plink
vcf
updated 1 day ago by
chrchang523
11k • written 2 days ago by
Smilesky
• 0
0
votes
0
replies
87
views
Why is the IC50 of the low-risk group always lower than that of the high-risk group?
OncoPredict
1 day ago by
nuorain
▴ 40
0
votes
0
replies
99
views
News:
Introduction to Epigenomics course
Epigenomics
RNA-seq
ATAC-seq
Chip-seq
HI-C
1 day ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
158
views
Remove batch effect RnaSeq (RUVg)
ruvg
batch
rnaseq
remove
1 day ago by
aLex97
• 0
0
votes
0
replies
103
views
Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R
dmp
methylkit
dmr
CpG
2 days ago by
egascon
▴ 60
1
vote
0
replies
195
views
Tool:
A rust binding for pairwise/multiple sequence aligner: bsalign-rs
bsalign
alignment
8 hours ago by
dwpeng
▴ 120
0
votes
2
replies
291
views
Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
DEG
CCLE
Melanoma
pyDESeq2
3 days ago by
mete.han.celebi
• 0
0
votes
0
replies
193
views
energy minimisation
Energy
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
swarnadurga66666m
• 0
0
votes
1
reply
223
views
How to concatenate different domains in the target database identified by hmmsearch
multiple
domains
hmmsearch
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Yongjie Zhang
▴ 110
0
votes
1
reply
233
views
How to filter Hmmsearch alignment
Hmmsearch
updated 3 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
Yongjie Zhang
▴ 110
2
votes
3
replies
2.3k
views
Defining residues as buried or exposed based in ASAs/RSAs
structural-bioinformatics
protein-biology
updated 4 days ago by
Dan A
• 0 • written 3.7 years ago by
Agenor Neto
▴ 10
1
vote
1
reply
256
views
Understanding Re-use of Query Sequences in Long Read Alignments
Alignment
PacBio
pbmm2
Minimap2
updated 4 days ago by
LauferVA
4.6k • written 4 days ago by
Charles-Alexandre Roy
▴ 50
0
votes
0
replies
188
views
Question about `vg construct`
vg
4 days ago by
zhengluo
• 0
0
votes
2
replies
331
views
Discrepancy between BAM and vcf
discrepancy
vcf
DRAGEN
updated 4 days ago by
Istvan Albert
102k • written 5 days ago by
louis-gil
• 0
2
votes
1
reply
445
views
Question about `vg giraffe`
vg
updated 5 days ago by
GenoMax
150k • written 6 days ago by
zhengluo
• 0
0
votes
1
reply
514
views
Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
small-RNASeq
miRNASeq
bowtie
miRDeep2
updated 5 days ago by
Ram
45k • written 9 months ago by
MIKA
• 0
3
votes
3
replies
411
views
How to align library of highly similar sequences
MPRA
variant
alignment
BWA
SNV
1 day ago by
rustyshackleford
• 0
0
votes
3
replies
1.6k
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 5 days ago by
Bastien Hervé
6.2k • written 22 months ago by
Sun
• 0
0
votes
1
reply
269
views
Reannotation of complete bacterial genome sequence
re-annotation
genome
whole
Automated
updated 2 days ago by
Juke34
9.2k • written 5 days ago by
csag6433
• 0
0
votes
2
replies
836
views
What are the best tools for quantifying allele-specific expression from bulk RNA-seq data these days?
ase
phASER
allele
gene
gatk
updated 5 days ago by
GenoMax
150k • written 5 days ago by
Paulo
• 0
3
votes
4
replies
3.3k
views
Lift over of GWAS summary stat file from Hg38 to Hg19
Hg38
linux
Liftover
GWAS
Hg19
updated 4 days ago by
Mllepnos
• 0 • written 3.8 years ago by
AVA
▴ 40
120,879 results • Page
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Answer: Issues with vg surject into paths
C: Strandedness Of Homer For Motif Analysis
Answer: Mapping vs Alignment
Answer: Issues with vg surject into paths
Comment: How to identify additional SNPs on EPICv2
Answer: How to identify additional SNPs on EPICv2
Comment: How to identify additional SNPs on EPICv2
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Comment: miRNA-seq normalization
by
GenoMax
150k
Did the kit use a specific miRNA adapter that was ligated? Were 10% alignments for reads that contained this adapter. Or is the 10% a fract…
Comment: Checking sex of a sample with sequencing data
by
ATpoint
87k
Checking whether you have signal on chrY would be a good start. That said, how can it be that you have data without info on the underlying …
Comment: DEG analysys using pseudobulk from single cell RNA-seq
by
Diego
▴ 110
Hi, Thanks for the input, Bastien. I agree with your comment. The problem is that the length of 3' between sps can be quite different. Ther…
Comment: miRNA-seq normalization
by
paulanavarrete116
• 0
Yes, the library construction was performed for small RNA by selecting for fragments of 18bp-30bp and sequencing SE50.
Comment: miRNA-seq normalization
by
GenoMax
150k
> Sperm data may contain fragmented reminiscent RNA and even RNA from bacteria that result in a low mapping percentage. and > as the % o…
Comment: Issues with vg surject into paths
by
GenoMax
150k
Please accept the answer (check mark) if it solved your problem to provide closure to this thread.
Answer: MULTIQC for miRNAseq data
by
i.sudbery
21k
I wouldn't pay much attention to the "status checks" section of the report. The thresholds they use for various things are rather arbitrary…
Answer: How to improve the mapping rate of vg giraffe
by
colindaven
7.3k
You'll get a lower mapping rate, but a higher number of perfect alignments. That is the improvement. You should get less heterozygous SNPs …
Comment: Issues with vg surject into paths
by
Rugare
• 0
That's very helpful, thank you!
Comment: miRNA-seq normalization
by
benformatics
4.1k
I disagree somewhat with this approach. For small RNA, there is a reasonable expectation of huge global differences between tissues and pot…
Comment: miRNA-seq normalization
by
ATpoint
87k
Neither. You make a count matrix containing only the RNA type you are looking for, and then consider the column sum the library size. Feed …
Comment: How to identify additional SNPs on EPICv2
by
Papyrus
★ 3.0k
I'm glad it worked for you! It's possible that some of them are meQTCL, although I think nearby or associated SNPs sometimes do not necessa…
Comment: Batch correction RNA-seq analysis
by
LauferVA
4.6k
this is a problem of perfect separation. if there are highly analogous data in a public repository, you may have *some* options, but gener…
Comment: DEG analysys using pseudobulk from single cell RNA-seq
by
Bastien Hervé
6.2k
If you are using the snRNA-seq protocol from 10X, you never get the full coverage of a gene but only 3' or 5' of it. So, I would say, genes…
Comment: Assign different color in same section of Chord diagram in R
by
Bastien Hervé
6.2k
In your example there is no information about this sub category you are mentioning using country names. The best would be to redesign your …
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