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120,888 results • Page
1 of 2418
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0
votes
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33
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Modify read groups in BAM file
samtools
BAM
picard
DRAGEN
updated 1 hour ago by
Istvan Albert
102k • written 1 hour ago by
Alex
• 0
0
votes
0
replies
41
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
4 hours ago by
ohtang7
▴ 40
4
votes
3
replies
229
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 4 hours ago by
Maximilian Haeussler
★ 1.7k • written 1 day ago by
shpak.max
▴ 50
0
votes
0
replies
46
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
5 hours ago by
karlensberg
• 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
9
replies
283
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 5 hours ago by
Pierre Lindenbaum
165k • written 1 day ago by
totoroGirl
• 0
1
vote
1
reply
110
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
5 hours ago by
Franck
• 0
0
votes
0
replies
39
views
Need help defining a threshold
DAVID
Genes
GO
5 hours ago by
Ana
• 0
2
votes
8
replies
290
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
updated 4 hours ago by
Istvan Albert
102k • written 1 day ago by
alexandrakortsi
• 0
2
votes
4
replies
147
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 10 hours ago by
ATpoint
87k • written 10 hours ago by
maplewj
▴ 20
0
votes
1
reply
279
views
Question about `vg construct`
vg
updated 13 hours ago by
Jouni Sirén
▴ 630 • written 5 days ago by
zhengluo
• 0
0
votes
0
replies
67
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
21 hours ago by
雨
▴ 20
0
votes
2
replies
232
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
4 hours 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 11 hours ago by
lieven.sterck
15k • written 12 months ago by
Matt
• 0
77
votes
31
replies
31k
views
18 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
7 hours ago by
Istvan Albert
102k
1
vote
4
replies
248
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
1 day ago by
dk7258859
• 0
4
votes
5
replies
202
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 1 day ago by
colindaven
7.3k • written 1 day ago by
harsh
▴ 20
0
votes
1
reply
152
views
MULTIQC for miRNAseq data
multiqc
updated 1 day ago by
i.sudbery
21k • written 1 day ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
152
views
How to improve the mapping rate of vg giraffe
vg
updated 1 day ago by
colindaven
7.3k • written 1 day ago by
gulin
• 0
0
votes
5
replies
211
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
updated 1 day ago by
GenoMax
150k • written 1 day ago by
paulanavarrete116
• 0
2
votes
2
replies
233
views
Issues with vg surject into paths
vg
updated 1 day ago by
GenoMax
150k • written 2 days ago by
Rugare
• 0
0
votes
0
replies
121
views
Missing short indels from vcf
bcftools
shortindels
mpileup
1 day ago by
kbranger
• 0
8
votes
12
replies
365
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 1 day ago by
LauferVA
4.6k • written 2 days ago by
ka132
▴ 10
0
votes
3
replies
175
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 1 day ago by
GenoMax
150k • written 1 day ago by
bge
• 0
0
votes
2
replies
178
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
1 day ago by
Diego
▴ 110
1
vote
1
reply
125
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 1 day ago by
GenoMax
150k • written 1 day ago by
ParastooA
▴ 20
0
votes
4
replies
209
views
Checking sex of a sample with sequencing data
ATAC-seq
11 hours ago by
xqyn
▴ 30
1
vote
5
replies
394
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 2 days ago by
Istvan Albert
102k • written 3 days ago by
shu8
• 0
1
vote
1
reply
144
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 2 days ago by
i.sudbery
21k • written 2 days ago by
ATS
• 0
2
votes
2
replies
297
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 11 hours ago by
lieven.sterck
15k • written 4 days ago by
Jl
• 0
1
vote
3
replies
190
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 2 days ago by
GenoMax
150k • written 2 days ago by
Ana
• 0
0
votes
1
reply
151
views
cant make the correct matrix
logfc
csv
updated 2 days ago by
lieven.sterck
15k • written 2 days ago by
Naila
• 0
1
vote
4
replies
209
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
2 days ago by
SomeOne
▴ 170
1
vote
7
replies
284
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 2 days ago by
yura.grabovska
▴ 750 • written 2 days ago by
zhang616123
• 0
0
votes
3
replies
211
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
updated 1 day ago by
Bastien Hervé
6.2k • written 2 days ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
117
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
2 days ago by
soledad.esteban
• 0
0
votes
4
replies
209
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 2 days ago by
ATpoint
87k • written 2 days ago by
ZuelTech
• 0
1
vote
14
replies
567
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 2 days ago by
colindaven
7.3k • written 3 days ago by
ZuelTech
• 0
1
vote
4
replies
1.2k
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 2 days ago by
swbarnes2
14k • written 4 days ago by
Wu-Sheng Zhang
• 0
1
vote
4
replies
278
views
Count matrices plotting
count
matrix
scanpy
2 days ago by
NIkita
• 0
3
votes
8
replies
322
views
Filter snRNA-seq .fastq files based on barcodes
snRNA-seq
scRNA-seq
FASTQ
bbmap
updated 2 days ago by
GenoMax
150k • written 2 days ago by
connorjfausto
▴ 30
0
votes
1
reply
198
views
Defining Sex Chromosomes in PLINK for a Camel Genome
plink
vcf
updated 2 days ago by
chrchang523
11k • written 3 days ago by
Smilesky
• 0
0
votes
0
replies
128
views
Why is the IC50 of the low-risk group always lower than that of the high-risk group?
OncoPredict
2 days ago by
nuorain
▴ 40
0
votes
0
replies
140
views
News:
Introduction to Epigenomics course
Epigenomics
RNA-seq
ATAC-seq
Chip-seq
HI-C
3 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
215
views
Remove batch effect RnaSeq (RUVg)
ruvg
batch
rnaseq
remove
2 days ago by
aLex97
• 0
0
votes
0
replies
145
views
Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R
dmp
methylkit
dmr
CpG
3 days ago by
egascon
▴ 60
1
vote
0
replies
234
views
Tool:
A rust binding for pairwise/multiple sequence aligner: bsalign-rs
bsalign
alignment
1 day ago by
dwpeng
▴ 120
0
votes
2
replies
342
views
Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
DEG
CCLE
Melanoma
pyDESeq2
5 days ago by
mete.han.celebi
• 0
0
votes
0
replies
230
views
energy minimisation
Energy
updated 5 days ago by
Pierre Lindenbaum
165k • written 5 days ago by
swarnadurga66666m
• 0
0
votes
1
reply
273
views
How to concatenate different domains in the target database identified by hmmsearch
multiple
domains
hmmsearch
updated 5 days ago by
GenoMax
150k • written 5 days ago by
Yongjie Zhang
▴ 110
120,888 results • Page
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Answer: Alternatives to UCSC genome browser for obtaining gene coordinates
Answer: Alternatives to UCSC genome browser for obtaining gene coordinates
Answer: Alternatives to UCSC genome browser for obtaining gene coordinates
Answer: Larger genome size than expected-please help
Answer: Larger genome size than expected-please help
Answer: cibersortx error - $ operator is invalid for atomic vectors
Comment: PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for vis
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Recent Replies
Answer: Modify read groups in BAM file
by
Istvan Albert
102k
I agree that the syntax and efficiency of read group handling in these tools are surprisingly convoluted. It would take me many tries to …
Comment: DiffBind normalization error: invalid argument type (list) - cannot make it work
by
buffealo
▴ 130
Thank you so much. Which metadata format should I proceed with, you think?
Comment: Larger genome size than expected-please help
by
Istvan Albert
102k
The critical thing to remember is that there will be information cannot be "proven" with your data because the read length imposes inherent…
Comment: Larger genome size than expected-please help
by
GenoMax
150k
There is nothing to prove per se. If you have multiple long reads in your data (advantage of nanopore over other short reads) that actually…
Answer: Alternatives to UCSC genome browser for obtaining gene coordinates
by
Maximilian Haeussler
★ 1.7k
Some people call what you want the "canonical" or "best" transcript. It's all documented here in UCSC's FAQ: https://genome.ucsc.edu/FAQ/FA…
Comment: Larger genome size than expected-please help
by
alexandrakortsi
• 0
Thank you very much for your response. There is a chance that what you are saying is correct, since every assembly method i've tried produc…
Answer: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
answer here: https://github.com/lindenb/jvarkit/issues/260 the depth was huge: $ samtools depth -r 'chrX:124068651-124068651' jet…
Answer: cibersortx error - $ operator is invalid for atomic vectors
by
Franck
• 0
I finally found the reason of the mistake. The initial scRNA seq dataset I used to generate the the signature matrix came from a paper and …
Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
by
Istvan Albert
102k
I am glad to hear that the post keeps on giving :-) Maybe the wording could have been the other way around, since keeping all pairs togeth…
Comment: PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for vis
by
Istvan Albert
102k
The tone was too nice :-) The bot thought it couldn't possibly be about bioinformatics
Comment: PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for vis
by
ATpoint
87k
Don't ask me why but the spam bot got triggered and suspended you. I reinstated you, not sure why that happened.
Answer: Larger genome size than expected-please help
by
colindaven
7.3k
Another possibility could be that the other assemblies are older. Nanopore seq tech has become very useful of late and generates good and l…
Comment: PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for vis
by
maplewj
▴ 20
Thank you so much for your kind and clear explanation, this really helped clarify what I was unsure about! I truly appreciate you taking th…
Answer: PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for vis
by
ATpoint
87k
> but I know vst is usually for RNA-seq It's just a transformation that unlocks the variance from the mean, you can use it here with no pr…
Comment: Checking sex of a sample with sequencing data
by
xqyn
▴ 30
can you give any thought? (scale:0-2000) ![ (can you give any thought?][1] [1]: /media/images/fa316655-e25e-46a6-adf6-15a5db66
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