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120,896 results • Page
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4
votes
6
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255
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated just now by
mmhryc
• 0 • written 2 days ago by
harsh
▴ 20
1
vote
2
replies
77
views
Choosing the best clustering method for a certain methylation data
DMR
k-means
hierarchical
clustering
methylation
updated 30 minutes ago by
5heikki
11k • written 7 hours ago by
Sophia
• 0
1
vote
4
replies
129
views
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 2 hours ago by
Billy Rowell
▴ 480 • written 7 hours ago by
jahnreinhard.ringger
• 0
0
votes
0
replies
23
views
How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR
RNA-seq
Batch
RSEM
effect
3 hours ago by
Apprentice
▴ 170
0
votes
11
replies
227
views
MultiQC_report
content_multiqc_fastqc
Quality_control_
Adapter
54 minutes ago by
AIMAR
• 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
2
votes
2
replies
124
views
Forum:
How to get into research for an absolute beginners
research
updated 5 hours ago by
GenoMax
150k • written 9 hours ago by
jpeduprep
• 0
0
votes
0
replies
50
views
News:
Online course — Comparative Genomics — 7–11 April
SNVs
ComparativeGenomics
SVs
GenomeAnnotation
9 hours ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
101
views
how to do a corellation analysis of multiple CRISPR data sets
batch-effect.
crispr
screen
correlation
5 hours ago by
Assa Yeroslaviz
★ 1.9k
8
votes
4
replies
333
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 6 hours ago by
LauferVA
4.6k • written 2 days ago by
shpak.max
▴ 60
1
vote
9
replies
288
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 51 minutes ago by
jared.andrews07
★ 18k • written 22 hours ago by
Will
• 0
0
votes
0
replies
83
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
opportunity
postdoc
21 hours ago by
Sophie
• 0
1
vote
2
replies
127
views
Modify read groups in BAM file
samtools
BAM
picard
DRAGEN
40 minutes ago by
Alex
• 0
0
votes
1
reply
127
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 11 hours ago by
zx8754
12k • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
90
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
1 day ago by
karlensberg
• 0
0
votes
9
replies
359
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 1 day ago by
Pierre Lindenbaum
165k • written 2 days ago by
totoroGirl
• 0
1
vote
1
reply
155
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
1 day ago by
Franck
• 0
0
votes
0
replies
80
views
Need help defining a threshold
DAVID
Genes
GO
1 day ago by
Ana
• 0
5
votes
9
replies
415
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
updated 12 hours ago by
colindaven
7.3k • written 2 days ago by
alexandrakortsi
• 0
5
votes
4
replies
212
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 1 day ago by
ATpoint
87k • written 1 day ago by
maplewj
▴ 20
0
votes
1
reply
311
views
Question about `vg construct`
vg
updated 1 day ago by
Jouni Sirén
▴ 630 • written 6 days ago by
zhengluo
• 0
0
votes
0
replies
100
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
1 day ago by
雨
▴ 20
0
votes
2
replies
319
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
1 day ago by
buffealo
▴ 130
1
vote
8
replies
1.5k
views
6 follow
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 1 day ago by
lieven.sterck
15k • written 12 months ago by
Matt
• 0
80
votes
32
replies
31k
views
18 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 4 hours ago by
Paulo
▴ 10 • written 11.1 years ago by
Istvan Albert
102k
1
vote
4
replies
298
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
2 days ago by
dk7258859
• 0
0
votes
1
reply
189
views
MULTIQC for miRNAseq data
multiqc
updated 2 days ago by
i.sudbery
21k • written 2 days ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
203
views
How to improve the mapping rate of vg giraffe
vg
updated 2 days ago by
colindaven
7.3k • written 2 days ago by
gulin
• 0
0
votes
5
replies
275
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
updated 2 days ago by
GenoMax
150k • written 2 days ago by
paulanavarrete116
• 0
2
votes
2
replies
274
views
Issues with vg surject into paths
vg
updated 2 days ago by
GenoMax
150k • written 3 days ago by
Rugare
• 0
0
votes
0
replies
154
views
Missing short indels from vcf
bcftools
shortindels
mpileup
2 days ago by
kbranger
• 0
8
votes
12
replies
432
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 2 days ago by
LauferVA
4.6k • written 3 days ago by
ka132
▴ 10
0
votes
3
replies
213
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 2 days ago by
GenoMax
150k • written 2 days ago by
bge
• 0
0
votes
2
replies
217
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
2 days ago by
Diego
▴ 110
1
vote
1
reply
158
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 2 days ago by
GenoMax
150k • written 2 days ago by
ParastooA
▴ 20
0
votes
4
replies
248
views
Checking sex of a sample with sequencing data
ATAC-seq
1 day ago by
xqyn
▴ 30
1
vote
5
replies
451
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 3 days ago by
Istvan Albert
102k • written 4 days ago by
shu8
• 0
1
vote
1
reply
178
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 3 days ago by
i.sudbery
21k • written 3 days ago by
ATS
• 0
2
votes
2
replies
335
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 1 day ago by
lieven.sterck
15k • written 5 days ago by
Jl
• 0
1
vote
5
replies
283
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 7 hours ago by
Istvan Albert
102k • written 3 days ago by
Ana
• 0
0
votes
1
reply
184
views
cant make the correct matrix
logfc
csv
updated 3 days ago by
lieven.sterck
15k • written 3 days ago by
Naila
• 0
1
vote
4
replies
250
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
3 days ago by
SomeOne
▴ 170
1
vote
7
replies
341
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 3 days ago by
yura.grabovska
▴ 760 • written 3 days ago by
zhang616123
• 0
0
votes
3
replies
246
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
updated 2 days ago by
Bastien Hervé
6.2k • written 3 days ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
151
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
3 days ago by
soledad.esteban
• 0
0
votes
4
replies
257
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 3 days ago by
ATpoint
87k • written 3 days ago by
ZuelTech
• 0
1
vote
14
replies
649
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 3 days ago by
colindaven
7.3k • written 4 days ago by
ZuelTech
• 0
1
vote
4
replies
1.5k
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 3 days ago by
swbarnes2
14k • written 5 days ago by
Wu-Sheng Zhang
• 0
1
vote
4
replies
329
views
Count matrices plotting
count
matrix
scanpy
3 days ago by
NIkita
• 0
3
votes
8
replies
371
views
Filter snRNA-seq .fastq files based on barcodes
snRNA-seq
scRNA-seq
FASTQ
bbmap
updated 2 days ago by
GenoMax
150k • written 3 days ago by
connorjfausto
▴ 30
120,896 results • Page
1 of 2418
Recent Votes
Answer: Modify read groups in BAM file
Answer: Extract length of sample sequence from vcf
Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
A: Extracting randomly subset of fastq reads from a huge file
Answer: Choosing the best clustering method for a certain methylation data
Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Comment: How to get into research for an absolute beginners
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Recent Replies
Answer: Choosing the best clustering method for a certain methylation data
by
5heikki
11k
[Affinity propagation][1] is the answer to all my clustering needs [1]: https://utstat.toronto.edu/reid/sta414/frey-affinity.pdf
Comment: Modify read groups in BAM file
by
Alex
• 0
Thanks Istvan, this seems like a reasonable enough solution that could be scripted across large batches of files. I'll give it a shot. Was …
Comment: MultiQC_report
by
AIMAR
• 0
No I don't, when I said errors I mean it shows 267 samples for the adapter content while I just have 50 samples of paired-end read = 100 re…
Comment: MultiQC_report
by
GenoMax
150k
> in this report multiqc missed 3 samples (6 reports ) and still made the error with the adapter content. Do you have any oddities in samp…
Answer: Extract length of sample sequence from vcf
by
Billy Rowell
▴ 480
This is hacky and definitely not prod ready, but if the goal is to get the length and not the sequence, you could use bcftools/paste/bc to …
Comment: Extract length of sample sequence from vcf
by
LauferVA
4.6k
you probably want to be working wihta bam file for this ..
Comment: MultiQC_report
by
AIMAR
• 0
![enter image description here][1] Here is the screenshot, in this report multiqc missed 3 samples (6 reports ) and still made the error…
Comment: Extract length of sample sequence from vcf
by
Istvan Albert
102k
Once you slice the reference genome, the positions in the VCF won't match the reference. For your method to work you would need to shift th…
Comment: Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
by
jared.andrews07
★ 18k
The source is this tool's literature review feature with the prompt "Impacts of AI on human creativity". The references contain some charac…
Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
by
Paulo
▴ 10
Thanks for the feedback, Istvan! Taking that into account, I made a few small tweaks and rewrote the script as follows: (I'm sharing it ju…
Comment: how to do a corellation analysis of multiple CRISPR data sets
by
Assa Yeroslaviz
★ 1.9k
I just modified my response. sorry for the missing information
Comment: Extract length of sample sequence from vcf
by
GenoMax
150k
> What I want to do is check how long sample A is for ex. the region 1:591173-591277 What do the CIGAR string(s) look like for reads in th…
Comment: Is there a tool to obtain GO terms for thousands of genes at once?
by
Istvan Albert
102k
The tool draws all ancestors for a term. I would say that, in general, it would be hard to avoid drawing common terms. Because they will st…
Comment: Shotgun dataset with polyG, low qualiity
by
shevch2009
• 0
Hi, Not really. Semibin gave me 100 bins, but they are all low quality, Commebin not working, trying to figure out why...
Answer: Choosing the best clustering method for a certain methylation data
by
yura.grabovska
▴ 760
Something like ConsensusClusterPlus will allow you to assess cluster stability directly via the report it produces. Smiliar for something l…
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