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121,524 results • Page
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0
votes
2
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29
views
Which Reference Hg38 or T2T?? Both??
Host
Removal
10 minutes ago by
Jon
• 0
3
votes
4
replies
94
views
NCBI Datasets CLI Question
ncbi-datasets
4 hours ago by
Bjorn
• 0
0
votes
0
replies
54
views
Incomplete assembly in HPRC dataset
pangenome
HPRC
reference
9 hours ago by
ohell
• 0
843
votes
170
replies
181k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 10 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
3
votes
3
replies
157
views
Joint Calling for Large Germline WGS Cohort
NGS
RAM
cohort
Genomics
WGS
updated 8 hours ago by
Jeremy Leipzig
23k • written 15 hours ago by
j.k3096
▴ 20
0
votes
4
replies
159
views
how shoud the phred score be intepreted?
sequencing
updated 8 hours ago by
GenoMax
152k • written 13 hours ago by
QX
▴ 70
0
votes
2
replies
242
views
Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be external SNPs?
WASP
15 hours ago by
jonas.andersson
▴ 40
0
votes
0
replies
58
views
Identifying RBP motifs overlapping exons
motifs
bedtools
RBP
15 hours ago by
RK
• 0
0
votes
0
replies
68
views
WGCNA analysis for Proteomics data
Proteomics
WGCNA
16 hours ago by
Sumit Paliwal
▴ 40
0
votes
0
replies
66
views
quality control for 16s metagenome reads
quality
metagneome
control
16s
fastp
16 hours ago by
m90
▴ 30
3
votes
8
replies
6.5k
views
7 follow
Cellranger count pipestance failed: The read lengths are incompatible with all the chemistries
10x
cellranger
single-cell
updated 17 hours ago by
zhang
• 0 • written 3.0 years ago by
firestar
★ 1.7k
0
votes
1
reply
526
views
News:
Hands-On Workshop - Next-Generation Sequencing Data Analysis: A Practical Introduction (September 10-12, 2025 in Berlin, Germany)
Workshop
RNA-Seq
Illumina
VariantCalling
DNA-Seq
18 hours ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
75
views
How to merge multiple pangenome graph files (generated by MC and PGGB)?
vg
pangenome
Minigraph-Cactus
PGGB
16 hours ago by
Yao
▴ 30
1
vote
0
replies
139
views
Can iHS and XP-EHH be applied to targeted sequencing data?
sequencing
targeted
ngs
ihs
2 days ago by
slzr_
▴ 10
1
vote
0
replies
149
views
Identify SNP, Indel variants from a List of FASTA sequence
SNP
2 days ago by
Trinh
▴ 10
2
votes
3
replies
278
views
PacBio amplicon reads partially aligned using minimap2 – library or analysis issue?
PacBio
minimap2
alignment
variants
pbmm2
4 hours ago by
louisflower1999
• 0
0
votes
0
replies
401
views
Job:
Biomedical Data Scientist / Systems Biologist / Omics Data Analyst / Bioinformatician / Computational Biologist (Tulane University, New Orleans, LA)
TUPulm
3 days ago by
yzhou40
• 0
0
votes
0
replies
200
views
Batch effect in codominant microsatellite data – how to correct
population-genetics
batch-effect
R
microsatellite
genotyping
3 days ago by
shervin
• 0
2
votes
3
replies
323
views
UCSC genome browser negative strand positions
Genomic
Data
Browser
UCSC
Visualization
Genome
updated 3 days ago by
Maximilian Haeussler
★ 1.8k • written 4 days ago by
ijarne
▴ 20
0
votes
1
reply
212
views
Error when computing bedtools bamtobed -bedpe
human
bedtools
libraries
illumina
bamtobed
updated 3 days ago by
ATpoint
88k • written 3 days ago by
María José
▴ 10
0
votes
9
replies
693
views
Ligand-Receptor analysis using LIANA - question about specificity
scRNA-seq
communication
cell-cell
updated 3 days ago by
Muhammad
▴ 10 • written 7 days ago by
abedkurdi10
▴ 190
2
votes
4
replies
1.2k
views
PRS calculation from two sample genotype results
prs
calculation
updated 3 days ago by
Muhammad
▴ 10 • written 6 months ago by
Arun
• 0
1
vote
16
replies
6.0k
views
PRS in UK Biobank - no covariate file and no phenotype file
UK
Biobank
PRS
3.8 years ago by
Jalil Sharif
▴ 80
39
votes
14
replies
2.6k
views
13 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
updated 3 days ago by
Анна
• 0 • written 5 months ago by
sviatoslav.kendall
▴ 980
0
votes
0
replies
151
views
News:
Introduction to Deep Learning for Biologists - online course, 3–7 November
MachineLearning
Python
deepLearning
ConvolutionalNeuralNetwork
3 days ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
789
views
Running trajectory and velocity analysis with multiple samples
seurat
velocity
loom
trajectory
written 15 months ago by
gogeni5529
▴ 70
2
votes
6
replies
497
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 3 days ago by
Gordon Smyth
★ 8.2k • written 4 days ago by
Guillermo
▴ 10
0
votes
1
reply
216
views
NMR modelling using xplor-NIH
peptide
xplor-NIH
NMR
3 days ago by
npk107
• 0
1
vote
4
replies
312
views
PCA interpretation
chip
seq
PCA
updated 5 hours ago by
swbarnes2
15k • written 4 days ago by
Irving
• 0
0
votes
0
replies
184
views
News:
course: Reproducibility in Bioinformatics - Only 2 seats remain!
Singularity
Git
Reproducibility
Docker
Snakemake
4 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
177
views
Annotate phylogenetic trees with bars or strips
otu
phylogenetics
R
taxonomy
metabarcoding
4 days ago by
Luca Arbore
▴ 10
2
votes
2
replies
381
views
Identifying Long Reads Spanning Chromosomal Breakpoints
ONT
samtools
Whole-Genome
updated 4 days ago by
trausch
★ 2.0k • written 6 days ago by
Noah
▴ 10
0
votes
2
replies
306
views
PAML output
PAML
Codeml
Selection
updated 1 day ago by
cfos4698
★ 1.1k • written 5 days ago by
Morjina
• 0
1
vote
0
replies
234
views
how to produce your own Nx plot
R
contiguity
plot
Nx
5 days ago by
Matteo Ungaro
▴ 130
1
vote
2
replies
350
views
Interpreting inconsistency between BLAST hits and phylogenetic clustering i
tree
phylogenetic
blast
4 days ago by
triplee0305
▴ 20
0
votes
0
replies
203
views
News:
Online course - Environmental Metagenomics - 13-17 October
Illumina
MAGs
Nanopore
Metagenomics
5 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
327
views
Deg Difference in Deseq2
Deg
updated 5 days ago by
swbarnes2
15k • written 5 days ago by
j.k.owaresat
• 0
0
votes
0
replies
243
views
No gene_trans_map file in CD-HIT-EST output
cd-hit-est
Trinity
RNAseq
Trinotate
updated 5 days ago by
GenoMax
152k • written 5 days ago by
ofarinas621
• 0
0
votes
3
replies
383
views
MultiQC report - unique reads from sequence counts
fastQC
unique
reads
multiQC
4 days ago by
Rozita
▴ 40
2
votes
3
replies
364
views
NCBI Reference Genomes
genomes
ncbi
updated 5 days ago by
GenoMax
152k • written 5 days ago by
anna
▴ 70
0
votes
0
replies
225
views
GATK HaplotypeCaller missed variants in amplicon gene panel data
amplicon
gene_panel
haplotypecaller
variant_calling
gatk
5 days ago by
Sofya
• 0
0
votes
1
reply
508
views
Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger multi with Combined Human-Mouse Reference
gem_classification
10x
cellranger_multi
combined_human-mouse_reference
updated 3 days ago by
GenoMax
152k • written 5 days ago by
tlallihuacan
• 0
0
votes
0
replies
213
views
Extracting logR and Baf files genome studio
Genomestudio
5 days ago by
1769mkc
★ 1.3k
0
votes
1
reply
389
views
Statistical analysis in a metagenomics study to validate biological differences
Metagenomics
analysis
updated 5 days ago by
chen
★ 2.5k • written 9 days ago by
Chijioke
• 0
1
vote
2
replies
585
views
Assembly issues
adapters
Assembly
Spades
updated 5 days ago by
chen
★ 2.5k • written 4 weeks ago by
anna
• 0
0
votes
5
replies
620
views
Trouble removing adapters from sequences using cutadapt
removal
cutadapt
adapter
primer
updated 5 days ago by
chen
★ 2.5k • written 11 days ago by
k.lagan
• 0
0
votes
5
replies
2.0k
views
Fastp
fastp
updated 5 days ago by
chen
★ 2.5k • written 3.2 years ago by
nishimalhotra2612
▴ 50
5
votes
10
replies
820
views
Need help using ExpansionHunter
ExpansionHunter
3 days ago by
brianhill_nc
• 0
0
votes
1
reply
286
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 4 days ago by
manaswwm
▴ 570 • written 5 days ago by
decorus
• 0
0
votes
0
replies
255
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
6 days ago by
Cassandra
• 0
121,524 results • Page
1 of 2431
Recent Votes
Answer: NCBI Datasets CLI Question
Answer: NCBI Datasets CLI Question
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Answer: NCBI Datasets CLI Question
SNP calling with SAMtools on multiple samples
Comment: Crac: Funny And/Or Weird Names For Bioinformatics Tools
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Recent Replies
Comment: Which Reference Hg38 or T2T?? Both??
by
Jon
• 0
The reference I'm having issues is the Naegleria Fowleri Karachi NF001, as this is the one that shows up in my samples. Everything I have …
Answer: Which Reference Hg38 or T2T?? Both??
by
GenoMax
152k
> So if I have my human sample and remove reads matching T2T, that Should? give me a host free set of reads??? For purpose of host deconta…
Comment: NCBI Datasets CLI Question
by
Bjorn
• 0
Thanks! Works great.
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
by
louisflower1999
• 0
Hi GenoMax, Thanks so much for your suggestion! Those amplicons are around 4.4kb. And there should be at least 1kb from the left and 800 b…
Comment: NCBI Datasets CLI Question
by
GenoMax
152k
Wanted to make it a complete answer with an additional command. Moved now.
Comment: NCBI Datasets CLI Question
by
Mensur Dlakic
★ 29k
Maybe make this an answer rather than a comment?
Comment: PCA interpretation
by
swbarnes2
15k
You are trying to PCA these by what, exactly? Binned coverage? Is this really informative?
Answer: NCBI Datasets CLI Question
by
GenoMax
152k
I don't see a way to specify a random number of accessions to download as an option. Perhaps you may want to open an issue and suggest that…
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
by
Zev.Kronenberg
12k
@genomax has a good point about trying `pbaa`. The tool will output consensus sequences of the different alleles. You can then use MSA to a…
Answer: Joint Calling for Large Germline WGS Cohort
by
Jeremy Leipzig
23k
Not to get too pedantic but joint genotyping solves a different problem (removing artefactual variants) from producing a population VCF tha…
Answer: Joint Calling for Large Germline WGS Cohort
by
DBScan
▴ 490
Another option would be HAILs VDS Combiner, [https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html#hail.vds.combiner.V…
Comment: how shoud the phred score be intepreted?
by
QX
▴ 70
thank you for explanation and documentation
Comment: how shoud the phred score be intepreted?
by
GenoMax
152k
Illumina sequencing assumes/generally expects that clusters in a sequencing field have an even distribution of ACTG so for every sequencing…
Comment: how shoud the phred score be intepreted?
by
QX
▴ 70
what do you mean by 'low nucleotide diversity'. If it is low nucleotide diversity, is it supposed to have consistent signals, leading to hi…
Answer: how shoud the phred score be intepreted?
by
GenoMax
152k
> Does the phred-score is affected by the position of the base in all the reads (vertical), or all the bases that belong to a single read (…
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