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120,984 results • Page
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0
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17
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Trouble when uploading FASTQ files on NCBI
upload
rnaseq
ncbi
updated 26 minutes ago by
GenoMax
150k • written 37 minutes ago by
Gerard
▴ 10
0
votes
2
replies
30
views
SyntaxError in file /snakefile, line 22: invalid decimal literal: None
python
error
syntax
snakemake
updated 1 minute ago by
Jesse
▴ 860 • written 1 hour ago by
Ana
• 0
2
votes
1
reply
122
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
updated 6 hours ago by
wojdyr
▴ 60 • written 1 day ago by
Shravya
• 0
0
votes
0
replies
58
views
News:
Course: Introduction to Genome Annotation (Online, 19–22 May 2025)
Gene-Prediction
Genome-Annotation
Gene-Models
7 hours ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
67
views
Error with running cellranger-atac count
cellranger
error
atac
single-cell
updated 2 hours ago by
GenoMax
150k • written 7 hours ago by
Khôi
• 0
836
votes
167
replies
173k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 2 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
80
views
HIC-pro with Forward and reverse reads not paired even when I use their test data.
HIC-pro
updated 1 hour ago by
GenoMax
150k • written 15 hours ago by
Aki
▴ 20
0
votes
1
reply
255
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
updated 16 hours ago by
Gordon Smyth
★ 7.9k • written 6 days ago by
Gerard
▴ 10
0
votes
0
replies
90
views
Job:
2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated 20 hours ago by
GenoMax
150k • written 20 hours ago by
Shicheng Guo
★ 9.6k
1
vote
2
replies
458
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
updated 20 hours ago by
GenoMax
150k • written 12 months ago by
Thomas
• 0
4
votes
10
replies
769
views
6 follow
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 21 hours ago by
cmdcolin
★ 4.2k • written 11 days ago by
jahnreinhard.ringger
• 0
0
votes
0
replies
86
views
Tutorial:
Fast SCENIC GRN Analysis with RegDiffusion
GRN
network
scRNA-seq
wgcna
23 hours ago by
Hao
▴ 10
2
votes
3
replies
526
views
Is it reasonable to do "Gene Regulatory Network Inference" for each cell type and do differential GRN
GRN
scRNA-seq
updated 23 hours ago by
Hao
▴ 10 • written 2.6 years ago by
shangguandong1996
▴ 30
1
vote
2
replies
283
views
Blastx issue
Long
coding
non
blastx
RNA
updated 1 day ago by
colindaven
7.4k • written 3 days ago by
Avik
• 0
2
votes
9
replies
444
views
TPM vs FPKM divergence at high values
tpm
fpkm
normalisation
updated 14 minutes ago by
Istvan Albert
102k • written 3 days ago by
megancgrdnr
• 0
3
votes
0
replies
108
views
Herald:
The Biostar Herald for Monday, April 14, 2025
herald
1 day ago by
Biostar
3.5k
0
votes
2
replies
251
views
What is the best way to know if a pair of genes is random?
terms
genes
go
8 hours ago by
Ana
• 0
1
vote
1
reply
198
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE
ChimeraX
AlphaFold
updated 1 day ago by
LauferVA
4.7k • written 3 days ago by
Picasa
▴ 680
1
vote
0
replies
83
views
News:
LAST CALL - Bioinformatics Pipeline Development with Nextflow - May 19-21, 2025 (online) - Apply Now
nextflow
rnaseq
workshop
1 day ago by
ecSeq Bioinformatics
▴ 20
1
vote
2
replies
208
views
RNA-seq, three comparisons - stick to one linear model, or use separate models?
statistics
mixed_effect_model
linear_model
stats
RNAseq
22 hours ago by
noodlejackson
▴ 40
0
votes
1
reply
120
views
Using Principal Components may muddle the detecting power of a GWAS?
q-value
covariates
genomic-inflation
pca
gwas
updated 1 day ago by
DBScan
▴ 470 • written 1 day ago by
AndrMod
• 0
0
votes
0
replies
98
views
Use Seed or Full Alignments from Pfam HMM as a filter step
hmm
sequences
metagenomic
1 day ago by
Janelyn123
• 0
3
votes
4
replies
262
views
Helicobacter pylori low-rate alignment
bioinformatics
transcriptomics
RNA-seq
updated 23 hours ago by
GenoMax
150k • written 2 days ago by
Ariadna
▴ 20
14
votes
3
replies
11k
views
Can The Wget Command Be Used To Download Pdbs
pdb
updated 1 day ago by
Calvin
• 0 • written 13.5 years ago by
Harpalss
▴ 310
0
votes
3
replies
281
views
Is a log2 transformation an essential step in preparing expression data for machine learning?
Machinelearning
microarray
preproccessing
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Sib
▴ 60
0
votes
2
replies
868
views
How to re-annotate the structure of gene against a known genomic file
RNA-Seq
updated 1 day ago by
Mensur Dlakic
★ 29k • written 5.9 years ago by
Kanoo
• 0
0
votes
2
replies
233
views
ONT Live-Basecalling Issue?
ONT
minKNOW
live-basecalling
updated 9 hours ago by
LauferVA
4.7k • written 2 days ago by
Akshay
• 0
3
votes
4
replies
282
views
Identify gene from sequence at scale in non-model organisms
name
sequence
gene
updated 2 days ago by
shelkmike
★ 1.5k • written 2 days ago by
matthewmerkin32
• 0
0
votes
0
replies
142
views
News:
Cellosaurus release 52 is available
database
line
cell
knowledgebase
biocuration
3 days ago by
Amos Bairoch
▴ 130
0
votes
2
replies
271
views
WGCNA
problem
updated 2 days ago by
GenoMax
150k • written 4 days ago by
香
• 0
0
votes
0
replies
267
views
Seeking Advice on Causal Inference for Treatment Effect Prediction (Small Sample, Genomic Covariates)
inference
causal
3 days ago by
oghzzang
▴ 50
5
votes
5
replies
446
views
Batch effect
RNAseq
Batch-Effect
2 days ago by
Fatemeh
▴ 40
0
votes
4
replies
382
views
convert Gene ID to Gene Symbol
gene-id
updated 3 days ago by
pinheirofabiano
▴ 110 • written 5 days ago by
majorprogeria
• 0
0
votes
1
reply
209
views
News:
Structural bioinformatics workshop
Structural
bioinformatics
updated 3 days ago by
GenoMax
150k • written 3 days ago by
reetesh
• 0
1
vote
10
replies
572
views
How to test the similarity of two gene expression profiles
test
gene
sets
updated 3 days ago by
JustinZhang
▴ 130 • written 4 days ago by
htchd
• 0
3
votes
3
replies
245
views
Which are the different kinds of GeneID that exist?
R
RNA-Seq
4 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
159
views
Error using DWLS
deconvolution
DWLS
RNAseq
4 days ago by
Ana
• 0
0
votes
5
replies
1.7k
views
How to remove this module selection error?
WGCNA
updated 4 days ago by
香
• 0 • written 2.3 years ago by
gupta00aritra
• 0
0
votes
1
reply
967
views
bbsplit : How to configure ambiguous/ambiguous2 parameters in order to consider as unmapped reads, reads mapped on both human/mouse references.
bbsplit
nextflow
updated 4 days ago by
GenoMax
150k • written 4 days ago by
ZheFrench
▴ 590
1
vote
2
replies
235
views
Limma for DEG aalysis
R
DEG
limma
ANALYSIS
4 days ago by
rahma.khoualdia
• 0
0
votes
0
replies
203
views
deletion impact
vcf
updated 4 days ago by
GenoMax
150k • written 4 days ago by
HarperReed
• 0
0
votes
2
replies
257
views
Help finding GTEx v8 file
GTEx
SHAPEIT2
3 days ago by
蒲蒲
• 0
2
votes
5
replies
304
views
Idat file processing issue with command line cli
CanineHTS
IDAT
4 days ago by
1769mkc
★ 1.2k
0
votes
0
replies
165
views
is there a way to get --ref paths to prioritize my order with vg call?
call
vg
vgcall
15 hours ago by
PolenP
• 0
0
votes
1
reply
224
views
Has anyone tried used simple ML models to identify virulence genes?
genetics
R
classifier
genomics
machinelearning
updated 4 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
Jack
• 0
0
votes
4
replies
344
views
What does vg autoindex mpmap do?
vg
mpmap
autoindex
1 day ago by
Ziyue
• 0
5
votes
4
replies
393
views
How to keep the same view for different AlphaFold 3 simulations in ChimeraX?
chimerax
alphafold
3
updated 3 days ago by
LauferVA
4.7k • written 4 days ago by
Picasa
▴ 680
0
votes
0
replies
185
views
filtering genes before or after the correlation?
co-expression
feature
selection
correlation
4 days ago by
tyasird
▴ 10
0
votes
16
replies
756
views
Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
cram
XA
compress
updated 4 days ago by
JustinZhang
▴ 130 • written 6 days ago by
Maarten
• 0
2
votes
4
replies
308
views
Which additional files are needed for the -taxids option in blast?
decontamination
taxids
blastn
updated 4 days ago by
GenoMax
150k • written 4 days ago by
WaspInSpace
• 0
120,984 results • Page
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Comment: makeblastdb Bus error
Answer: Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcom
Answer: MULTIQC for miRNAseq data
Answer: Should I scale all genes in single cell Seurat?
Answer: scRNA-seq downstream analysis on raw vs batch corrected counts
Comment: Snakemake Global Environment Container
Answer: How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
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Recent Replies
Comment: SyntaxError in file /snakefile, line 22: invalid decimal literal: None
by
Jesse
▴ 860
That's [Python's f-string](https://docs.python.org/3/tutorial/inputoutput.html#formatted-string-literals), which in this case just turns `{…
Comment: TPM vs FPKM divergence at high values
by
Istvan Albert
102k
I admit I had no firm idea what a TPM vs FPKM plot might look like. I never computed both, but this motivated me enough to take a salmon …
Comment: Trouble when uploading FASTQ files on NCBI
by
GenoMax
150k
This may be hard to help/diagnose for biostar community since we don't know about your local set up. Problem could be on either end (your o…
Comment: TPM vs FPKM divergence at high values
by
dariober
15k
Yes, the axes are both logarithmic, the difference is in the input data with FPKM being log'd and TPM being raw.
Comment: SyntaxError in file /snakefile, line 22: invalid decimal literal: None
by
ATpoint
87k
I am not a SnakeMake person but what is the `f` supposed to be? `f'/{{...`
Comment: TPM vs FPKM divergence at high values
by
Istvan Albert
102k
I think both are logarithmic axes. Just one is in exponential notation the other is not.
Comment: HIC-pro with Forward and reverse reads not paired even when I use their test dat
by
GenoMax
150k
Looks like the original dataset has an equal number of records based on the lines so that input looks correct. $ wc -l SRR400264_* …
Comment: MULTIQC for miRNAseq data
by
Alana Conceição Maia Lessa
• 0
Thank you so much!
Comment: Error with running cellranger-atac count
by
GenoMax
150k
> Before processing the fastq files with the count command, I was trimming primer & linker sequences according to a paper I was looking at.…
Comment: TPM vs FPKM divergence at high values
by
ATpoint
87k
Good catch, that makes sense. As I said above, mathematically I don't see a reason for a non-linear relationship if on normal scale, and I …
Comment: DWLS error Dmat and dvec are incompatible!
by
Ana
• 0
Hi, I am having the same issue. Were you able to solve it? Thanks in advance.
Comment: TPM vs FPKM divergence at high values
by
dariober
15k
Looking at the range of the data, it seems your input FPKM is very likely on the log scale, i.e. your input is log(FPKM). The TPM data inst…
Answer: Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcom
by
wojdyr
▴ 60
Parsers work with file syntax, so generally there are no mmCIF parsers for enzymes or for receptor proteins, just parsers for mmCIF files. …
Comment: Snakemake Global Environment Container
by
meetmet
▴ 10
Many thanks! I completely missed this option. Cheers.
Comment: What is the best way to know if a pair of genes is random?
by
Ana
• 0
Thank you so much
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