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121,320 results • Page
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HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 33 minutes ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
27
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
3 hours ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
1.9k
views
normalize between 2 different platform
RNA-Seq
updated 10 hours ago by
1364454115
• 0 • written 8.4 years ago by
Edalat
▴ 30
0
votes
0
replies
50
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
bioinformatics
analysis
10 hours ago by
1364454115
• 0
838
votes
170
replies
179k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
0
votes
1
reply
104
views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated 19 hours ago by
GenoMax
151k • written 20 hours ago by
michael.dhar
• 0
2
votes
4
replies
381
views
Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in terms of using repetitive elements to filter peaks
sequence
scatac
cell
single
10xatac
15 hours ago by
gynecoloji
• 0
0
votes
2
replies
177
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
21 hours ago by
Sd
• 0
0
votes
0
replies
87
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
1 day ago by
a58c4637
• 0
7
votes
5
replies
236
views
nanopore unaligned bam files
nanopore
updated 22 hours ago by
GenoMax
151k • written 1 day ago by
sarahmanderni
▴ 130
0
votes
0
replies
78
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
1 day ago by
gogeni5529
▴ 70
0
votes
1
reply
129
views
Issue with Package installation in R.
R
GCC
updated 18 hours ago by
GenoMax
151k • written 1 day ago by
harsh
▴ 20
0
votes
0
replies
77
views
MAPQ algorithms of Giraffe
giraffe
vg
1 day ago by
gulin
• 0
5
votes
4
replies
544
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 1 day ago by
colindaven
7.6k • written 9 days ago by
biostars
▴ 30
0
votes
1
reply
125
views
IGV view for Chromatin accessibility ATAC-seq
ATAC-seq
updated 1 day ago by
ATpoint
88k • written 1 day ago by
Vxike
• 0
2
votes
2
replies
1.7k
views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell
scATAC-Seq
Signac
transcriptomics
updated 1 day ago by
Jan
• 0 • written 3.6 years ago by
patelk26
▴ 340
4
votes
2
replies
177
views
WGCNA blockwiseModules function for small datasets
WGCNA
blockwiseModules
20 hours ago by
ATS
▴ 10
1
vote
4
replies
207
views
How to add GFP in STAR reference?
STAR
updated 1 day ago by
GenoMax
151k • written 1 day ago by
bioinfo
▴ 160
0
votes
0
replies
110
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
1 day ago by
emil.paulitz
• 0
0
votes
0
replies
107
views
News:
Population Genomics Using Ancient DNA Data course
DemographicModels
PopulationGenomics
aDNA
Genomics
1 day ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
140
views
Can you compare GETx and TCGA miRNA non normalized counts a
comapre
to
how
updated 1 day ago by
ATpoint
88k • written 1 day ago by
radwa_noreen
• 0
0
votes
3
replies
250
views
ATAC-seq analysis
ATAC-seq
Samtools
Sorting
updated 1 day ago by
ATpoint
88k • written 2 days ago by
SEJAL
• 0
0
votes
1
reply
169
views
Learn tNGS
tNGS
updated 1 day ago by
GenoMax
151k • written 2 days ago by
hang
• 0
4
votes
3
replies
306
views
Server Requirements for long read data analysis
longreadserver
longreadanalysis
serverrequirements
Server
updated 2 days ago by
colindaven
7.6k • written 3 days ago by
genomics_student
• 0
0
votes
1
reply
174
views
The molecular signatures database (MSigDB) in R
MSigDB
updated 2 days ago by
marco.barr
▴ 170 • written 2 days ago by
Kelly
• 0
2
votes
3
replies
558
views
plotProfile Errors of DiffBind
DiffBind
2 days ago by
lijiangres
▴ 20
0
votes
0
replies
146
views
Job:
Lab Head positions at the WEHI, Melbourne Australia
LabHead
Australia
JobPosting
2 days ago by
Gordon Smyth
★ 8.1k
0
votes
0
replies
135
views
Merging single ATAC seq data sets from multiple sample
10x
2 days ago by
1769mkc
★ 1.3k
1
vote
3
replies
249
views
GSEA analysis in R
R
ranked_list
GSEA
updated 2 days ago by
ATpoint
88k • written 2 days ago by
rajdeepboral00
▴ 70
0
votes
1
reply
175
views
Assembly issues
adapters
Assembly
Spades
updated 2 days ago by
GenoMax
151k • written 2 days ago by
anna
• 0
2
votes
8
replies
442
views
Use taxdb tp get scientific names in local BLAST output
taxdb
sscinames
taxonomy
makeblastdb
blast
updated 2 days ago by
GenoMax
151k • written 3 days ago by
Luca Arbore
▴ 10
1
vote
7
replies
2.4k
views
Search all SRA data for sequence? Raw reads only
SRA
NCBI
Raw reads
fastq
updated 2 days ago by
Wayne
★ 2.1k • written 4.3 years ago by
poppersrules
▴ 10
2
votes
2
replies
245
views
Forum:
Is this Rosalind inspired project actually useful?
python
code-review
2 days ago by
Andrew
• 0
1
vote
1
reply
163
views
Subset a GAM (graph alignment) file
pangenome
vg
vgteam
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Pau
• 0
0
votes
0
replies
148
views
News:
Reproducibility in Bioinformatics course
Conda
Singularity
Docker
Snakemake
Nextflow
2 days ago by
Physalia-courses
★ 2.6k
1
vote
0
replies
186
views
Any tips for optimizing an all vs all alignment with minimap2
mapping
nanopore
genomics
minimap2
2 days ago by
Mark
▴ 60
0
votes
0
replies
143
views
Mismatch in orthology results from local alignment and phylogenetic analysis.
alignment
local
Phylogeny
global
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Shakunthala Natarajan
• 0
2
votes
1
reply
190
views
How to automate blasting contigs?
assembly
contig
blast
WGS
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
marongiu.luigi
▴ 740
0
votes
0
replies
155
views
Are there tools to find differences in biochemical pathways between organisms?
biochemistry
bioinformatics
differential
pathways
updated 1 day ago by
colindaven
7.6k • written 3 days ago by
marongiu.luigi
▴ 740
0
votes
0
replies
145
views
DiffBind plot.profile error
DiffBind
BiocParallel
3 days ago by
this_is_me_trying
• 0
0
votes
3
replies
774
views
News:
9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- FINAL CALL --
Workshop
RNA-Seq
transcriptomics
VariantCalling
DNA-Seq
3 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
3
replies
477
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 3 days ago by
ATpoint
88k • written 8 days ago by
bioinfo
▴ 160
0
votes
1
reply
385
views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
updated 3 days ago by
agis.maulana12
• 0 • written 7 days ago by
Wenhai
• 0
3
votes
4
replies
330
views
miRNA Quantifiaction Tool
quatification
mirna
updated 3 days ago by
GenoMax
151k • written 3 days ago by
anthony.santana.703.j
▴ 30
1
vote
3
replies
324
views
WGCNA pickSoftThreshold problem
picksoftthreshold
question
problem
wgcna
updated 20 hours ago by
LChart
5.0k • written 4 days ago by
ton_of_questions
• 0
7
votes
6
replies
381
views
Fungal Annotation Comparison
Annotation
RNAseq
Fungus
genome_assembly
funannotate
updated 3 days ago by
colindaven
7.6k • written 4 days ago by
SomeOne
▴ 180
0
votes
1
reply
298
views
Is comparing seeds sufficient, or should alignments be compared instead?
readmapping
updated 4 days ago by
shenwei356
8.7k • written 4 days ago by
curiousfellow@123
• 0
7
votes
2
replies
500
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
updated 4 days ago by
colindaven
7.6k • written 10 days ago by
anna
▴ 70
2
votes
1
reply
313
views
Clustering on Big data (100 million samples)
Clustering
Data
Learning
Big
Machine
updated 4 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
Rushikesh
▴ 10
7
votes
7
replies
2.2k
views
6 follow
Where can I find a vcf file with individuals in it, that have a specific disease?
Phenotype
VCF
written 17 months ago by
Patrick
▴ 30
121,320 results • Page
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WGCNA modules and categorical traits relationship
Comment: nanopore unaligned bam files
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
Answer: WGCNA blockwiseModules function for small datasets
Answer: WGCNA blockwiseModules function for small datasets
A: bcftools selest sites with FILTER "PASS" or "."
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Answer: HOMER findMotifsGenome.pl failed compilation
by
文杰
• 0
I use the commamd `conda install perl==5.32.1 ` solve this problem
Comment: normalize between 2 different platform
by
1364454115
• 0
Hello, Could you please tell me whether different datesets generated by multiplex PCR and 5'UMI-tagged 5′-RACE can be analyzed together? T…
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
gynecoloji
• 0
Thanks for your response. I think it may be better to keep those repetitive regions and only filter out the blacklisted regions. This is a …
Comment: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
jared.andrews07
★ 18k
IDR addresses a different problem than removal of reads aligning to blacklist reads, though it's unquestionably useful for deriving more ro…
Comment: Issue with Package installation in R.
by
GenoMax
151k
Simply posting a snippet of error message in a question is the reason you have not received any responses. Please make an effort to formu…
Answer: Building database with snpEff -- -gtf22 option not recognized/file not read
by
michael.dhar
• 0
Based on the ordering of the commands here: https://github.com/pcingola/SnpEff/issues/583 I believe I just needed to place the "build" c…
Comment: WGCNA blockwiseModules function for small datasets
by
ATS
▴ 10
That's great to know. Thanks for your input!
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
LChart
5.0k
It should be noted that concerns about mapping artifacts in ChIP-seq really come from an era where reads were 36bp (or even 25bp!) in lengt…
Comment: WGCNA pickSoftThreshold problem
by
LChart
5.0k
AGain you seem to be over-filtering. Your mean.k and median.k are really low, so I think the number of input genes you used for this is ver…
Answer: Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in t
by
jared.andrews07
★ 18k
I am going to guess you've seen/thoroughly read [this paper about the ENCODE blacklist regions](https://www.nature.com/articles/s41598-019-…
Comment: Using VEP custom input
by
Sd
• 0
Initially, I converted the file to GFF3 format in order to run VEP, but I got warnings and couldn’t figure out what the problem was. GFF…
Comment: nanopore unaligned bam files
by
colindaven
7.6k
When you have a bam make sure you check the methyl tags MM and ML are present. Something like samtools view -h x.bam | grep MM sam…
Comment: nanopore unaligned bam files
by
sarahmanderni
▴ 130
yes keeping both mapping info and methylation info at the same time is the intention. Thanks so much for the reosponse! I will try it
Comment: nanopore unaligned bam files
by
GenoMax
151k
> OP wants to align AND keep the methylation info Then use something like minimap2 -t use_N_cores -Y -y -ax map-ont your_minimap_ind…
Comment: nanopore unaligned bam files
by
lieven.sterck
15k
I think OP wants to align AND keep the methylation info, which is indeed the tricky part ... Not entirely sure but I think the `dorado ali…
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