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120,997 results • Page
1 of 2420
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Picard : Bait_interval and Target_interval
read_depth_measure
Picard_tool
Bed_file
coverage
just now by
AIMAR
• 0
2
votes
2
replies
108
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
5 hours ago by
lushjia
• 0
0
votes
0
replies
51
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
11 hours ago by
Sd
• 0
0
votes
0
replies
68
views
Question about Calculation of Dietary index in the NHANES Database
index
DI-GM
Dietary
NHANES
18 hours ago by
城玮
• 0
836
votes
167
replies
173k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
0
replies
67
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
18 hours ago by
Matt
• 0
0
votes
1
reply
153
views
Detection SNPs and Indels Bacteria
SNPs
updated 21 hours ago by
Istvan Albert
102k • written 1 day ago by
Eltercertopico
• 0
1
vote
4
replies
324
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
19 hours ago by
Fatemeh
▴ 40
0
votes
1
reply
117
views
Different number of fragments after doublets removal in each run
ArchR
updated 22 hours ago by
Bastien Hervé
6.2k • written 1 day ago by
Bioinformatics_16
• 0
0
votes
0
replies
79
views
Seeking Guidance on Next Steps for DNA Methylation Biomarker Screening in Cancer Prognosis
early-cancer-screening
TCGA
Epigenomics
DNA-Methylation
cancer-prognosis
1 day ago by
Riley J
• 0
0
votes
1
reply
130
views
Help with Panel of Normal (PON)
somatic-mutation
PoN
updated 21 hours ago by
Ram
45k • written 1 day ago by
TJ
• 0
4
votes
2
replies
228
views
Why don't I see people calculating FPKM from normalized read counts?
normalization
RNA-seq
updated 21 hours ago by
ATpoint
87k • written 1 day ago by
shelkmike
★ 1.5k
1
vote
7
replies
348
views
Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).
EPI2ME
MEDAKA
updated 16 hours ago by
GenoMax
150k • written 1 day ago by
Anurag
• 0
0
votes
0
replies
76
views
freebayes with pools of different number of individuals
freebayes
poolseq
1 day ago by
Jeanlain
• 0
0
votes
3
replies
178
views
Insight into Trimmomatic
Trimmomatic
Trimming
Reads
updated 1 day ago by
GenoMax
150k • written 1 day ago by
jh5ym
• 0
0
votes
3
replies
177
views
Trouble when uploading FASTQ files on NCBI
rnaseq
ncbi
1 hour ago by
Gerard
▴ 10
1
vote
4
replies
232
views
SyntaxError in file /snakefile, line 22: invalid decimal literal: None
python
snakemake
updated 18 hours ago by
Jesse
▴ 870 • written 1 day ago by
Ana
▴ 10
3
votes
2
replies
234
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
1 day ago by
Shravya
• 0
0
votes
0
replies
117
views
News:
Course: Introduction to Genome Annotation (Online, 19–22 May 2025)
Gene-Prediction
Genome-Annotation
Gene-Models
2 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
148
views
Error with running cellranger-atac count
cellranger
atac
single-cell
updated 1 day ago by
Ram
45k • written 2 days ago by
Khôi
• 0
0
votes
2
replies
210
views
HIC-pro with Forward and reverse reads not paired even when I use their test data.
HIC-pro
1 day ago by
Aki
▴ 20
1
vote
1
reply
317
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
updated 2 days ago by
Gordon Smyth
★ 7.9k • written 7 days ago by
Gerard
▴ 10
0
votes
0
replies
161
views
Job:
2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated 2 days ago by
GenoMax
150k • written 2 days ago by
Shicheng Guo
★ 9.6k
1
vote
2
replies
510
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
updated 2 days ago by
GenoMax
150k • written 12 months ago by
Thomas
• 0
4
votes
10
replies
835
views
6 follow
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 2 days ago by
cmdcolin
★ 4.2k • written 12 days ago by
jahnreinhard.ringger
• 0
0
votes
0
replies
146
views
Tutorial:
Fast SCENIC GRN Analysis with RegDiffusion
GRN
network
scRNA-seq
wgcna
2 days ago by
Hao
▴ 10
2
votes
3
replies
606
views
Is it reasonable to do "Gene Regulatory Network Inference" for each cell type and do differential GRN
GRN
scRNA-seq
updated 2 days ago by
Hao
▴ 10 • written 2.6 years ago by
shangguandong1996
▴ 30
1
vote
2
replies
365
views
Blastx issue
blastx
lncRNA
updated 1 day ago by
Ram
45k • written 5 days ago by
Avik
• 0
2
votes
9
replies
581
views
TPM vs FPKM divergence at high values
tpm
fpkm
normalisation
updated 1 day ago by
Istvan Albert
102k • written 5 days ago by
megancgrdnr
• 0
3
votes
0
replies
162
views
Herald:
The Biostar Herald for Monday, April 14, 2025
herald
2 days ago by
Biostar
3.5k
1
vote
2
replies
311
views
What is the best way to know if a pair of genes is random?
go-terms
genes
updated 1 day ago by
Ram
45k • written 6 days ago by
Ana
▴ 10
1
vote
1
reply
250
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE
ChimeraX
AlphaFold
updated 2 days ago by
LauferVA
4.7k • written 5 days ago by
Picasa
▴ 680
1
vote
0
replies
134
views
News:
LAST CALL - Bioinformatics Pipeline Development with Nextflow - May 19-21, 2025 (online) - Apply Now
nextflow
rnaseq
workshop
3 days ago by
ecSeq Bioinformatics
▴ 20
1
vote
2
replies
261
views
RNA-seq, three comparisons - stick to one linear model, or use separate models?
statistics
mixed-effect-model
stats
RNAseq
linear-model
updated 1 day ago by
Ram
45k • written 3 days ago by
noodlejackson
▴ 40
1
vote
1
reply
191
views
Using Principal Components may muddle the detecting power of a GWAS?
q-value
covariates
genomic-inflation
pca
gwas
updated 3 days ago by
DBScan
▴ 480 • written 3 days ago by
AndrMod
• 0
0
votes
0
replies
146
views
Use Seed or Full Alignments from Pfam HMM as a filter step
hmm
sequences
metagenomic
3 days ago by
Janelyn123
• 0
3
votes
4
replies
325
views
Helicobacter pylori low-rate alignment
RNA-seq
transcriptomics
updated 1 day ago by
Ram
45k • written 3 days ago by
Ariadna
▴ 20
14
votes
3
replies
11k
views
Can The Wget Command Be Used To Download Pdbs
pdb
updated 3 days ago by
Calvin
• 0 • written 13.5 years ago by
Harpalss
▴ 310
0
votes
3
replies
347
views
Is a log2 transformation an essential step in preparing expression data for machine learning?
Machine-learning
preproccessing
microarray
updated 1 day ago by
Ram
45k • written 4 days ago by
Sib
▴ 60
0
votes
2
replies
920
views
How to re-annotate the structure of gene against a known genomic file
RNA-Seq
updated 3 days ago by
Mensur Dlakic
★ 29k • written 5.9 years ago by
Kanoo
• 0
0
votes
2
replies
292
views
ONT Live-Basecalling Issue?
ONT
minKNOW
live-basecalling
updated 2 days ago by
LauferVA
4.7k • written 4 days ago by
Akshay
• 0
3
votes
4
replies
338
views
Identify gene from sequence at scale in non-model organisms
sequence
gene
updated 1 day ago by
Ram
45k • written 4 days ago by
matthewmerkin32
• 0
0
votes
0
replies
195
views
News:
Cellosaurus release 52 is available
biocuration
database
knowledgebase
cell-line
updated 1 day ago by
Ram
45k • written 4 days ago by
Amos Bairoch
▴ 130
0
votes
2
replies
327
views
WGCNA
WGCNA
updated 1 day ago by
Ram
45k • written 5 days ago by
香
• 0
0
votes
0
replies
470
views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
causal-inference
updated 1 day ago by
Ram
45k • written 5 days ago by
oghzzang
▴ 50
5
votes
5
replies
505
views
Batch effect
RNAseq
Batch-Effect
3 days ago by
Fatemeh
▴ 40
0
votes
4
replies
441
views
convert Gene ID to Gene Symbol
gene-id
updated 5 days ago by
pinheirofabiano
▴ 110 • written 7 days ago by
majorprogeria
• 0
0
votes
1
reply
260
views
News:
Structural bioinformatics workshop
Structural-bioinformatics
updated 1 day ago by
Ram
45k • written 5 days ago by
reetesh
• 0
1
vote
10
replies
643
views
How to test the similarity of two gene expression profiles
gene-sets
updated 1 day ago by
Ram
45k • written 6 days ago by
htchd
• 0
3
votes
3
replies
301
views
Which are the different kinds of GeneID that exist?
R
RNA-Seq
5 days ago by
pinheirofabiano
▴ 110
120,997 results • Page
1 of 2420
Recent Votes
A: Alignment and mapping
A: Alignment and mapping
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
HISAT2 V.S. STAR
Answer: Does vg giraffe output secondary and supplimentary alignments?
Answer: Does vg giraffe output secondary and supplimentary alignments?
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Recent Replies
Comment: Trimming nanopore reads
by
dalibenam64
• 0
Hello, Can I skip trimming my reads since I'm filtering them by taking those with the highest scores using fastp? I'm performing variant ca…
Comment: Trouble when uploading FASTQ files on NCBI
by
Gerard
▴ 10
Thanks to those who replied, the problem is solved and I'll just mention it in case anybody gets the same problem : Actually despite the "C…
Comment: Does vg giraffe output secondary and supplimentary alignments?
by
lushjia
• 0
Thank you so much for the information! It's really helpful!
Answer: Does vg giraffe output secondary and supplimentary alignments?
by
Jouni Sirén
▴ 660
There is option `--max-multimaps INT`, which makes Giraffe output at most `INT` alignments for each read. We don't really test it, but it s…
Comment: How do I figure out pangenome location of hg38 coordinates?
by
lushjia
• 0
There should be GRCh38 paths in the pggb graph. You can check the paths in the graph by extracting P or W lines: > zcat <gfa.gz> | grep …
Comment: Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-
by
GenoMax
150k
> I tried HAC & SUP both did not work for me. What did not work? You actually need to recall the bases using HAC/SUP models and `dorado` b…
Comment: Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-
by
Anurag
• 0
hey, thank you for reply still i am getting same error.
Comment: Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-
by
Anurag
• 0
Thank you for replying and the tip! I tried HAC & SUP both did not work for me.
Comment: SyntaxError in file /snakefile, line 22: invalid decimal literal: None
by
Jesse
▴ 870
That all makes sense! My best guess is something totally unexpected from somewhere else in the file and it's reporting the wrong line. (I…
Comment: protease candidates for my protein of interest
by
Fatemeh
▴ 40
Thanks very much, but this only gives some bacterial enzymes that can cut my protein, unfortunately. I was thinking maybe there are some p…
Answer: Detection SNPs and Indels Bacteria
by
Istvan Albert
102k
The breseq pipeline is a good start https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing other alternatives exi…
Comment: protease candidates for my protein of interest
by
GenoMax
150k
Not as comprehensive as above but there is also `pepdigest` from EMBOSS: https://www.bioinformatics.nl/cgi-bin/emboss/pepdigest
Comment: Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-
by
GenoMax
150k
If you have the run data folder available then you should go back and re-call the bases using either HAC (high accuracy) or preferably SUP …
Answer: protease candidates for my protein of interest
by
Elisabeth Gasteiger
★ 2.4k
Have you tried PeptideCutter? https://web.expasy.org/peptide_cutter/
Comment: Help with Panel of Normal (PON)
by
GenoMax
150k
There were two opinions about this in a past thread: https://www.biostars.org/p/9575107/ You can find the 1000 genomes hg38 PON here: http…
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