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120,874 results • Page
1 of 2418
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Votes
Replies
6
votes
11
replies
148
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated just now by
swbarnes2
14k • written 5 hours ago by
ka132
• 0
0
votes
3
replies
43
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 26 minutes ago by
GenoMax
150k • written 2 hours ago by
bge
• 0
0
votes
1
reply
21
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 10 minutes ago by
GenoMax
150k • written 43 minutes ago by
shpak.max
▴ 50
0
votes
0
replies
16
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
1 hour ago by
Diego
▴ 110
1
vote
1
reply
23
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 50 minutes ago by
GenoMax
150k • written 1 hour ago by
ParastooA
▴ 20
0
votes
0
replies
16
views
Checking sex of a sample with sequencing data
ATAC-seq
1 hour ago by
xqyn
▴ 30
0
votes
0
replies
18
views
MULTIQC for miRNAseq data
multiqc
2 hours ago by
Alana Conceição Maia Lessa
• 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
5
replies
276
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 6 hours ago by
Istvan Albert
102k • written 2 days ago by
shu8
• 0
1
vote
1
reply
69
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 6 hours ago by
i.sudbery
21k • written 6 hours ago by
ATS
• 0
0
votes
2
replies
96
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
updated 4 hours ago by
GenoMax
150k • written 8 hours ago by
dk7258859
• 0
0
votes
1
reply
179
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 7 hours ago by
lieven.sterck
15k • written 2 days ago by
Jl
• 0
1
vote
3
replies
112
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 8 hours ago by
GenoMax
150k • written 9 hours ago by
Ana
• 0
0
votes
1
reply
81
views
cant make the correct matrix
logfc
csv
updated 9 hours ago by
lieven.sterck
15k • written 10 hours ago by
Naila
• 0
1
vote
4
replies
122
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
8 hours ago by
SomeOne
▴ 170
1
vote
7
replies
182
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 10 hours ago by
yura.grabovska
▴ 750 • written 12 hours ago by
zhang616123
• 0
0
votes
2
replies
102
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
8 hours ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
52
views
Issues with vg surject into paths
vg
11 hours ago by
Rugare
• 0
0
votes
0
replies
53
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
13 hours ago by
soledad.esteban
• 0
0
votes
4
replies
134
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 15 hours ago by
ATpoint
87k • written 15 hours ago by
ZuelTech
• 0
1
vote
14
replies
396
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 15 hours ago by
colindaven
7.3k • written 1 day ago by
ZuelTech
• 0
1
vote
4
replies
837
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 21 hours ago by
swbarnes2
14k • written 3 days ago by
Wu-Sheng Zhang
• 0
1
vote
4
replies
195
views
Count matrices plotting
count
matrix
scanpy
12 hours ago by
NIkita
• 0
3
votes
8
replies
201
views
Filter snRNA-seq .fastq files based on barcodes
snRNA-seq
scRNA-seq
FASTQ
bbmap
updated 2 hours ago by
GenoMax
150k • written 23 hours ago by
connorjfausto
▴ 30
0
votes
1
reply
120
views
Defining Sex Chromosomes in PLINK for a Camel Genome
plink
vcf
updated 1 day ago by
chrchang523
11k • written 1 day ago by
Smilesky
• 0
0
votes
0
replies
66
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
79
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
137
views
Remove batch effect RnaSeq (RUVg)
ruvg
batch
rnaseq
remove
11 hours ago by
aLex97
• 0
0
votes
0
replies
84
views
Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R
dmp
methylkit
dmr
CpG
1 day ago by
egascon
▴ 60
1
vote
0
replies
172
views
Tool:
A rust binding for pairwise/multiple sequence aligner: bsalign-rs
bsalign
alignment
20 hours ago by
dwpeng
▴ 120
0
votes
2
replies
259
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
173
views
energy minimisation
Energy
updated 3 days ago by
Pierre Lindenbaum
165k • written 3 days ago by
swarnadurga66666m
• 0
0
votes
1
reply
203
views
How to concatenate different domains in the target database identified by hmmsearch
multiple
domains
hmmsearch
updated 3 days ago by
GenoMax
150k • written 3 days ago by
Yongjie Zhang
▴ 110
0
votes
1
reply
209
views
How to filter Hmmsearch alignment
Hmmsearch
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 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 3 days ago by
Dan A
• 0 • written 3.7 years ago by
Agenor Neto
▴ 10
1
vote
1
reply
233
views
Understanding Re-use of Query Sequences in Long Read Alignments
Alignment
PacBio
pbmm2
Minimap2
updated 3 days ago by
LauferVA
4.6k • written 3 days ago by
Charles-Alexandre Roy
▴ 50
0
votes
0
replies
169
views
Question about `vg construct`
vg
3 days ago by
zhengluo
• 0
0
votes
2
replies
304
views
Discrepancy between BAM and vcf
discrepancy
vcf
DRAGEN
updated 4 days ago by
Istvan Albert
102k • written 4 days ago by
louis-gil
• 0
2
votes
1
reply
424
views
Question about `vg giraffe`
vg
updated 4 days ago by
GenoMax
150k • written 5 days ago by
zhengluo
• 0
0
votes
1
reply
495
views
Difference in mapping rate when aligned with mapper.pl of miReep2 and bowtie1
small-RNASeq
miRNASeq
bowtie
miRDeep2
updated 4 days ago by
Ram
45k • written 9 months ago by
MIKA
• 0
3
votes
3
replies
385
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 4 days ago by
Bastien Hervé
6.2k • written 22 months ago by
Sun
• 0
0
votes
1
reply
246
views
Reannotation of complete bacterial genome sequence
re-annotation
genome
whole
Automated
updated 1 day ago by
Juke34
9.2k • written 5 days ago by
csag6433
• 0
0
votes
2
replies
814
views
What are the best tools for quantifying allele-specific expression from bulk RNA-seq data these days?
ase
phASER
allele
gene
gatk
updated 4 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
8
votes
3
replies
382
views
How do I install Terminal on Windows?
Terminal
updated 5 days ago by
5heikki
11k • written 5 days ago by
phyms
• 0
1
vote
1
reply
249
views
Mapping reversion mutations
NGS
reversion
mutation
updated 5 days ago by
Ram
45k • written 5 days ago by
reddyraghuveer664
• 0
0
votes
0
replies
205
views
Issue with Fetching Population Allele Frequency in gnomAD GraphQL API
allelle
frequency
api
GraphQL
gnomad
5 days ago by
DareDevil
★ 4.4k
0
votes
1
reply
252
views
Attempts to demultiplex long reads from .pod5 result in unclassified reads
dorado
sequencing
Long-read
demultiplex
updated 5 days ago by
GenoMax
150k • written 5 days ago by
Placeholder@12654926
• 0
0
votes
1
reply
280
views
Issue with BSgenomeForge::forgeBSgenomeDataPkgFromNCBI
R
BSgenomeForge
BSgenome
NCBI
updated 5 days ago by
ATpoint
87k • written 5 days ago by
noodle
▴ 650
120,874 results • Page
1 of 2418
Recent Votes
Comment: Filter snRNA-seq .fastq files based on barcodes
Comment: Filter snRNA-seq .fastq files based on barcodes
Answer: Tools for clustering genes rather than samples for bulk RNA-seq
Comment: Microarray platform probrID to Circ-ID problem
BLAST, setting maximum number of hits
Comment: Batch correction RNA-seq analysis
Comment: Batch correction RNA-seq analysis
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Recent Replies
Comment: bbduk.sh trimming to BAM output file
by
GenoMax
150k
BBMap is actively maintained but what you have is an edge case. You can try writing to Brian Bushnell (his email can be found in software i…
Answer: Alternatives to UCSC genome browser for obtaining gene coordinates
by
GenoMax
150k
Get the basic gene annotation from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/GRCh37_mapping/gencode.v47lift37.ba…
Comment: bbduk.sh trimming to BAM output file
by
bge
• 0
Hi, I appreciate the confirmation -- I worry that I mess up. Anyway, the input uBAM file has a tag with the barcode+umi sequences req…
Comment: Microarray platform probrID to Circ-ID problem
by
GenoMax
150k
This appears to be a commercially available array. You could contact Arraystar and see if they would be willing to share the annotations: h…
Answer: bbduk.sh trimming to BAM output file
by
GenoMax
150k
Using a uBAM input and writing uBAM output is indeed not working directly. Probably because it is an edge case that @Brian likely did not t…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
GenoMax
150k
Use the 10x's BAM splitting tool (https://github.com/10XGenomics/subset-bam ). You should share those BAM's (instead of fastq) since they h…
Comment: Filter snRNA-seq .fastq files based on barcodes
by
connorjfausto
▴ 30
> What is the intent behind doing this? From our original snRNA-seq Seurat object, we have a small subset (~5% of nuclei) that collaborato…
Comment: Batch correction RNA-seq analysis
by
GenoMax
150k
Since you are stuck with what you have keep this is as another variable (hopefully it is same as two sequencer batches). Generally people (…
Comment: Batch correction RNA-seq analysis
by
ka132
• 0
Unfortunately, I just found out the libraries were prepped separately as well. Thanks for the advice!
Comment: Batch correction RNA-seq analysis
by
ka132
• 0
Well, dangit - I just heard back and the same sequencer was used but library prep was done separately. Bummer. Thanks for the assistance.
Comment: Batch correction RNA-seq analysis
by
jared.andrews07
★ 18k
Batch correction as you mention shouldn't even run, I expect ComBat-seq will yell at you about confounded covariates if you try. But as me…
Comment: Batch correction RNA-seq analysis
by
ka132
• 0
The actual experiment and collection of samples were done at same time. Library prep was definitely done by same person using same protocol…
Comment: Batch correction RNA-seq analysis
by
GenoMax
150k
There should be no appreciable batch effect because of sequencing, as long as following is true. The same sequencer (or at least type i.e. …
Comment: Batch correction RNA-seq analysis
by
ka132
• 0
yeah.... this is what I was afraid of. I wish this was a lesson that I needed to learn, but again I had no input on the processing up to th…
Comment: Batch correction RNA-seq analysis
by
ka132
• 0
Just sequencing, no common control unfortunately.
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