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121,282 results • Page
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Job:
Ensembl Genebuild Project Leader, EMBL-EBI, Hinxton near Cambridge, UK
Ensembl
jobs
updated 20 minutes ago by
GenoMax
151k • written 2 hours ago by
A@Ensembl
▴ 30
2
votes
6
replies
435
views
Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
macs2
cutandrun
chipseq
updated 30 minutes ago by
GenoMax
151k • written 5 days ago by
sk
• 0
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
1
reply
51
views
tools to increase hi-c resolution
resolution
hi-c
updated 3 hours ago by
GenoMax
151k • written 4 hours ago by
J.F.Jiang
▴ 930
0
votes
1
reply
53
views
How to fix this this tangle in my bacterial genome assembly
misassembly
assembly
genomics
ngs
updated 12 minutes ago by
GenoMax
151k • written 6 hours ago by
Mark
▴ 30
5
votes
2
replies
278
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 5 hours ago by
colindaven
7.5k • written 4 days ago by
biostars
▴ 30
0
votes
4
replies
146
views
Help configuring RepeatMasker
human
illumina
libraries
RepeatMasker
updated 4 hours ago by
Michael
55k • written 7 hours ago by
María José
▴ 10
0
votes
2
replies
555
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 11 hours ago by
David Langenberger
11k • written 4 weeks ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
64
views
Clustering on Big data (100 million samples)
Clustering
Data
Learning
Big
Machine
11 hours ago by
Rushikesh
• 0
0
votes
1
reply
78
views
How to process Iso-Seq files in SRA public fastqs
Iso-seq
updated 6 hours ago by
GenoMax
151k • written 11 hours ago by
Abieskawa
• 0
14
votes
19
replies
8.1k
views
10 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 12 hours ago by
Prash
▴ 290 • written 5.0 years ago by
Eugene A
▴ 190
2
votes
0
replies
109
views
EggNOG-mapper problem
all
Hi
updated 18 hours ago by
GenoMax
151k • written 1 day ago by
Salma
▴ 20
0
votes
0
replies
79
views
Colsep for dendrogram and ColSideColors in heatmap.2
Heatmap
DGE
EdgeR
heatmap.2
1 day ago by
fabian
▴ 10
1
vote
1
reply
154
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
379
views
Why am I getting the exact same MarkDuplicates results when passing a query or coordinate sorted bam?
picard
bwa
updated 3 hours ago by
GenoMax
151k • written 2 days ago by
curious
▴ 890
0
votes
2
replies
212
views
use AverageExpression to stratify samples
scRNA
3 hours ago by
ndra1456
• 0
0
votes
0
replies
148
views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
3 days ago by
Wenhai
• 0
0
votes
0
replies
751
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
175
views
RepeatMasker output file question
RepeatMasker
3 days ago by
xinguok794
• 0
3
votes
1
reply
467
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
304
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
299
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
278
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
253
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
228
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 3 days ago by
Ram
45k • written 4 days ago by
bioinfo
▴ 160
2
votes
3
replies
316
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
258
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
370
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
277
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
246
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
426
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
418
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
375
views
Biological meaning of metrics commonly used for QC in scRNA-seq?
ribosome
QC
velocity
single-cell
intron
updated 4 days ago by
jared.andrews07
★ 18k • written 5 days ago by
txema.heredia
▴ 240
0
votes
0
replies
184
views
News:
Eukaryotic eDNA Metabarcoding Course (14–18 July, Online)
Metabarcoding
eDNA
Genomics
Nanopore
5 days ago by
Physalia-courses
★ 2.6k
7
votes
12
replies
734
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 10 days ago by
npont
• 0
0
votes
0
replies
194
views
eHOMD database: Ref seq Aligned FASTA vs Full RefSeq?
HOMD
database
5 days ago by
bioinfo
▴ 60
2
votes
3
replies
445
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
359
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
244
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
282
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
5 days ago by
anna
▴ 40
0
votes
4
replies
410
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
536
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
224
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 6 days ago by
s.faria
• 0 • written 2.7 years ago by
Gerard
▴ 10
2
votes
4
replies
688
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
346
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
357
views
Comparing sets of genes for similarity
R
jaccard
genes
marker
clustering
4 days ago by
yura.grabovska
▴ 780
0
votes
0
replies
251
views
News:
Network Analysis in Systems Biology - 2 seats left
Bioconductor
SystemsBiology
R
NetworkAnalysis
RNAseq
6 days ago by
Physalia-courses
★ 2.6k
121,282 results • Page
1 of 2426
Recent Votes
Answer: Phased haplotype using WGS data from Nebula Genomics and GATK
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
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Recent Replies
Comment: How to fix this this tangle in my bacterial genome assembly
by
GenoMax
151k
> I'm wondering what I should do at this stage? Was this assembly done with short or long reads? If no long reads were used then doing som…
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
by
sk
• 0
![overall view ][1] ![view at a peak location called by macs2][2] [1]: /media/images/70777c0b-f219-4be9-9ac5-dde78d66 [2]: /media/i…
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
by
jared.andrews07
★ 18k
As @atpoint has repeatedly said, actually *look at the data*. What does it look like in IGV? If you cannot see numerous obvious peaks **by …
Comment: use AverageExpression to stratify samples
by
ndra1456
• 0
It concerns me because the AggregrateExpression function is also known for pseudobulk analysis and I am not sure which is the best way. A…
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
by
sk
• 0
I re-ran the CUT&RUN data analysis pipeline with adjusted filtering criteria and used a finer bin size of 5 for BAM coverage generation. Th…
Comment: Why am I getting the exact same MarkDuplicates results when passing a query or
by
GenoMax
151k
> Maybe MarkDuplicates treats supplementary duplicates as part of the same duplicate "event" as their primary and doesn’t count them separa…
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…
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