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121,281 results • Page
1 of 2426
Sort: Rank
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Votes
Replies
2
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4
replies
376
views
Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
macs2
cutandrun
chipseq
just now by
sk
• 0
0
votes
1
reply
22
views
tools to increase hi-c resolution
resolution
hi-c
updated 28 minutes ago by
GenoMax
151k • written 46 minutes ago by
J.F.Jiang
▴ 930
0
votes
0
replies
31
views
How to fix this this tangle in my bacterial genome assembly
misassembly
assembly
genomics
ngs
2 hours ago by
Mark
▴ 30
4
votes
2
replies
263
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 2 hours ago by
colindaven
7.5k • written 4 days ago by
biostars
▴ 30
0
votes
4
replies
100
views
Help configuring RepeatMasker
human
illumina
libraries
RepeatMasker
updated 46 minutes ago by
Michael
55k • written 4 hours ago by
María José
▴ 10
837
votes
170
replies
178k
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
2
replies
548
views
News:
9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- SUMMER IN BERLIN --
Workshop
RNA-Seq
transcriptomics
VariantCalling
DNA-Seq
updated 7 hours ago by
David Langenberger
11k • written 4 weeks ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
56
views
Clustering on Big data (100 million samples)
Clustering
Data
Learning
Big
Machine
8 hours ago by
Rushikesh
• 0
0
votes
1
reply
64
views
How to process Iso-Seq files in SRA public fastqs
Iso-seq
updated 2 hours ago by
GenoMax
151k • written 8 hours ago by
Abieskawa
• 0
14
votes
19
replies
8.1k
views
10 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 9 hours ago by
Prash
▴ 290 • written 5.0 years ago by
Eugene A
▴ 190
2
votes
0
replies
101
views
EggNOG-mapper problem
all
Hi
updated 15 hours ago by
GenoMax
151k • written 21 hours ago by
Salma
▴ 20
0
votes
0
replies
74
views
Colsep for dendrogram and ColSideColors in heatmap.2
Heatmap
DGE
EdgeR
heatmap.2
1 day ago by
fabian
▴ 10
1
vote
1
reply
147
views
Decision making on choosing the based on tblastn result
interpretation
tblastn
BLAST
E-score
updated 1 day ago by
GenoMax
151k • written 1 day ago by
srestha
• 0
9
votes
7
replies
2.9k
views
How to Identify the pathogenicity of a set of variants (by using ACMG guidelines)?
pathogenicity
SNP
variants
updated 2 days ago by
Damianos P. Melidis
▴ 60 • written 6.5 years ago by
DanielC
▴ 210
0
votes
4
replies
342
views
Why am I getting the exact same MarkDuplicates results when passing a query or coordinate sorted bam?
picard
bwa
updated just now by
GenoMax
151k • written 2 days ago by
curious
▴ 890
0
votes
1
reply
180
views
use AverageExpression to stratify samples
scRNA
updated 7 hours ago by
ATpoint
88k • written 2 days ago by
ndra1456
• 0
0
votes
0
replies
144
views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
2 days ago by
Wenhai
• 0
0
votes
0
replies
731
views
Multiple taxonomy hits per OTU ID in VSEARCH despite --top_hits_only (90% ID after QIIME2 clustering at 97%)
vsearch
updated 3 days ago by
GenoMax
151k • written 3 days ago by
salma.sarker
• 0
0
votes
0
replies
166
views
RepeatMasker output file question
RepeatMasker
3 days ago by
xinguok794
• 0
3
votes
1
reply
460
views
Which GWAS tool to use that can work on Czech cases and British controls, on a binary trait?
plink2
gwas
saige
updated 3 days ago by
LChart
4.9k • written 5 days ago by
anita.szabo08
▴ 10
1
vote
2
replies
298
views
Unsure whether or not I overcorrected for batch effect in dataset
Quality
Plot
PCA
Control
updated 2 days ago by
GenoMax
151k • written 3 days ago by
Megan
▴ 60
0
votes
3
replies
292
views
Primer removal in amplicon sequencing
removal
Primer
Amplicon
DADA2
sequencing
updated 3 days ago by
GenoMax
151k • written 3 days ago by
sxf520
• 0
0
votes
1
reply
274
views
GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no “chr”)
GATK
VCF
BSQR
updated 3 days ago by
Ram
45k • written 3 days ago by
iamsmor
• 0
0
votes
1
reply
249
views
Batch correction without biological covariates
Combat-seq
RNA-seq
batch-correction
updated 3 days ago by
Ram
45k • written 4 days ago by
as823jk
• 0
0
votes
1
reply
224
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 3 days ago by
Ram
45k • written 3 days ago by
bioinfo
▴ 160
2
votes
3
replies
312
views
RagTag results
NGS
scaffolding
RagTag
gaps
updated 4 days ago by
shelkmike
★ 1.6k • written 4 days ago by
synthiiihuh
• 0
0
votes
1
reply
254
views
Tools that output positions of matching kmers
sequences
genomics
kmers
updated 4 days ago by
GenoMax
151k • written 4 days ago by
gil.hornung
▴ 100
2
votes
4
replies
363
views
mitochondrial assamply use NOVOplasty
mitochondrial
genome
mammles
updated 4 days ago by
cfos4698
★ 1.1k • written 5 days ago by
m90
▴ 30
0
votes
2
replies
274
views
Still bad phred score after fastp
phred
fastp
updated 3 days ago by
Ram
45k • written 4 days ago by
Shazel
• 0
0
votes
1
reply
241
views
Cytohubba problem and difference networks
Network
cytoscape
cytohubba
analysis
updated 4 days ago by
Scooter
▴ 310 • written 5 days ago by
mastorehpournazari
• 0
0
votes
1
reply
422
views
Cytoscape KEGG plots reverting to original layout after changing style or column
kegg
cytoscape
updated 4 days ago by
Scooter
▴ 310 • written 26 days ago by
Adrian
• 0
2
votes
4
replies
413
views
Mass-spectrometry proteomics
Proteomics
analysis
updated 2 days ago by
Gordon Smyth
★ 8.1k • written 4 days ago by
Nasim Gandomdoust
• 0
7
votes
3
replies
369
views
Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome
QC
velocity
single-cell
intron
updated 3 days ago by
jared.andrews07
★ 18k • written 4 days ago by
txema.heredia
▴ 240
0
votes
0
replies
180
views
News:
Eukaryotic eDNA Metabarcoding Course (14–18 July, Online)
Metabarcoding
eDNA
Genomics
Nanopore
4 days ago by
Physalia-courses
★ 2.6k
7
votes
12
replies
727
views
miRNA low mapping(Qiagen miRNA Library Prep)
Qiagen
pipeline
trimming
alignment
miRNA
updated 4 days ago by
GenoMax
151k • written 7 days ago by
anthony.santana.703.j
▴ 10
0
votes
12
replies
1.0k
views
STAR alignment not detecting some transcripts / custom reference
star
bwa
rna-seq
alignment
scrna-seq
updated 4 days ago by
rfran010
★ 1.5k • written 9 days ago by
npont
• 0
0
votes
0
replies
188
views
eHOMD database: Ref seq Aligned FASTA vs Full RefSeq?
HOMD
database
5 days ago by
bioinfo
▴ 60
2
votes
3
replies
440
views
pysam header and body
bam
pysam
view
updated 5 days ago by
dariober
15k • written 6 days ago by
Matteo Ungaro
▴ 120
4
votes
1
reply
353
views
Discrepency in assembly sizes
Pacbio
assembly
Kmer
updated 5 days ago by
shelkmike
★ 1.6k • written 6 days ago by
hpapoli
▴ 170
0
votes
1
reply
240
views
fasterq-dump fails before completing lookup
lookup
incomplete
fasterq-dump
updated 5 days ago by
GenoMax
151k • written 5 days ago by
nmannda148
• 0
4
votes
1
reply
278
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
5 days ago by
anna
▴ 40
0
votes
4
replies
405
views
ATACSEQ normlization for bigwig files
normalization
atac-seq
updated 5 days ago by
ATpoint
88k • written 5 days ago by
RD
▴ 20
6
votes
6
replies
529
views
finding gene sequence from WGS data
gene
WGS
updated 3 days ago by
swbarnes2
15k • written 5 days ago by
analyst
▴ 70
0
votes
0
replies
220
views
Question about Protein-protein-DNA complex prediction
prediction
protein
5 days ago by
mickley413
• 0
1
vote
10
replies
2.1k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 5 days ago by
s.faria
• 0 • written 2.7 years ago by
Gerard
▴ 10
2
votes
4
replies
683
views
RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis
method
rnaseq
updated 6 days ago by
mbyvcm
▴ 460 • written 11 days ago by
cgibbsm
▴ 20
1
vote
2
replies
343
views
pddg+odgi+vg to perform pangenome analysis to cyanobacteria
odgi
pggb
help
pangenome
vg
updated 6 days ago by
GenoMax
151k • written 6 days ago by
snmdba
▴ 10
1
vote
2
replies
354
views
Comparing sets of genes for similarity
R
jaccard
genes
marker
clustering
4 days ago by
yura.grabovska
▴ 780
0
votes
0
replies
246
views
News:
Network Analysis in Systems Biology - 2 seats left
Bioconductor
SystemsBiology
R
NetworkAnalysis
RNAseq
6 days ago by
Physalia-courses
★ 2.6k
2
votes
5
replies
494
views
Running Unicycler with a merged fastq file
unicycler
bacterial-genome
assembly
updated 4 days ago by
GenoMax
151k • written 6 days ago by
Assa Yeroslaviz
★ 1.9k
121,281 results • Page
1 of 2426
Recent Votes
A: How To Uncompress The 1000 Genome Vcf.Gz File
A: In Sam Format, Clarify The Meaning Of The "0" Flag.
C: In Sam Format, Clarify The Meaning Of The "0" Flag.
Comment: Decision making on choosing the based on tblastn result
Answer: Which GWAS tool to use that can work on Czech cases and British controls, on a b
Comment: RagTag results
Unsure whether or not I overcorrected for batch effect in dataset
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Recent Replies
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
curious
▴ 890
I think I figured this out (maybe). It looks like MarkDuplicates is marking supplementary reads as duplicates in the query-sorted CRAM, but…
Comment: tools to increase hi-c resolution
by
GenoMax
151k
> none of them can directly output files in .hic or .mcool formats. `Juicer` (https://github.com/aidenlab/juicer/wiki ) outputs `.hic` fil…
Comment: Help configuring RepeatMasker
by
Michael
55k
Also: "I've downloaded the Dfam-7.hmm.gz.md5"? This is (only) the checksum for the Dfam-7.hmm.gz file. You may want to download the Dfam-7.…
Comment: Help configuring RepeatMasker
by
GenoMax
151k
As @michael noted above, you will need to run the `configure` program after installing with conda.
Answer: Phased haplotype using WGS data from Nebula Genomics and GATK
by
colindaven
7.5k
I would ask Nebula to reanalyze `person1.vcf` for you, since you show it was aligned against a different reference so is not compatible. …
Comment: Help configuring RepeatMasker
by
María José
▴ 10
Thanks @michaeld, although I download RepeatMasker with conda.
Comment: How to process Iso-Seq files in SRA public fastqs
by
GenoMax
151k
> But lima seems to not take any computation resources to process, and only show that it is running when I use "jobs". What does this mean…
Answer: Help configuring RepeatMasker
by
Michael
55k
There's a configure script in the RepeatMasker distribution. From the documentation: https://www.repeatmasker.org/RepeatMasker/ Run Config…
Comment: use AverageExpression to stratify samples
by
ATpoint
88k
You *can* do that, but more information would be necessary to explain your open-ended question more. Why do you think it biases analysis? A…
Answer: 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- S
by
David Langenberger
11k
**I would like to introduce you to our invited speakers:** ---------- ![enter image description here][1] **Prof. Dr. Helene Kr…
Answer: ACMG assignment tools
by
Prash
▴ 290
Great points, there! I'd like to employ KAVIAR and Sherloc guidelines , APIs if available. Unfortunately, KAVIAR guidelines are not upda…
Comment: Decision making on choosing the based on tblastn result
by
GenoMax
151k
What is your aim here? Asking the right question will ensure that you get the correct answer. Query coverage is important. Other hits may …
Comment: VCF2MAF structural variant file issue.
by
eebloom
▴ 90
I have the same issue, did you find a solution?
Comment: de novo chromosome level assembly
by
colindaven
7.5k
Look at Ragtag on github, assuming you have a close reference to align against. Else your main option is spending more on Hi-C data. Else m…
Comment: Currently recommended Oxford Nanopore data basecalling and preprocessing pipelin
by
Asan Emirsale
• 0
the `dorado` does remove adapters for only 10.4.1 etc data. If you have data from r9.4.1, you should activate `---trim` flag. I suggest al…
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