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121,015 results • Page
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Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
updated just now by
GenoMax
150k • written 29 minutes ago by
RJDan
• 0
0
votes
3
replies
656
views
HOMER Motif Analysis-- homer2 error
rna-seq
homer
updated 35 minutes ago by
ATpoint
87k • written 15 months ago by
HypoGG
• 0
1
vote
0
replies
42
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
4 hours ago by
Biostar
3.5k
0
votes
4
replies
101
views
Forum:
ELISA‑Focused Lab Management & Analysis App – Would You Use It?
help
biotech
startup
updated 4 hours ago by
GenoMax
150k • written 7 hours ago by
Novoo
• 0
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
0
replies
93
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
CancerPhylogenetics
ChromosomalInstability
18 hours ago by
Bingxin
• 0
0
votes
1
reply
182
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 1 day ago by
Jasim
• 0 • written 2 days ago by
omicon
▴ 40
1
vote
3
replies
376
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Sib
▴ 60
0
votes
0
replies
106
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 1 day ago by
GenoMax
150k • written 1 day ago by
Abieskawa
• 0
0
votes
3
replies
334
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Novoo
• 0
1
vote
1
reply
235
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 18 hours ago by
Michael
55k • written 3 days ago by
Chatchapon
• 0
1
vote
4
replies
297
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
vladimir_vinarsky
• 0
0
votes
2
replies
196
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
1 day ago by
andrebolerbarros
• 0
0
votes
4
replies
326
views
UCSC's NCBI RefSeq Track tables: header differences
ucsc-genome-browswer
refseq
ncbi
3 days ago by
Synanth
• 0
2
votes
2
replies
1.3k
views
How do you do differential splicing using edgeR command diffSpliceDGE?
differential-splicing
diffSpliceDGE
edger
updated 2 days ago by
Gordon Smyth
★ 7.9k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
168
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
3 days ago by
gagi1993
• 0
0
votes
1
reply
222
views
Issue with Agilent 2100 BioAnalyzer HS DNA Assay Trace
library-preparation
DNA
bioanalyzer
updated 3 days ago by
GenoMax
150k • written 3 days ago by
Beatrice
• 0
1
vote
2
replies
745
views
QIAseq 16S/ITS Screening Panel Primers?
16s
primers
metagenomics
ITS
updated 3 days ago by
GenoMax
150k • written 3.2 years ago by
Isaac
• 0
2
votes
1
reply
287
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
updated 3 days ago by
Zhenyu Zhang
★ 1.3k • written 5 days ago by
Matt
• 0
1
vote
3
replies
327
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Sd
• 0
0
votes
0
replies
294
views
Trouble with CIBERSORTx: All P-values > 0.05, Low Correlation, High RMSE – What Could Be Going Wrong?
R
CIBERSORTx
CIBERSORT
script
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Pumla
• 0
0
votes
1
reply
214
views
How can I identify genes with the MSTRG notation?
R
stringtie
RNA-Seq
updated 4 days ago by
GenoMax
150k • written 4 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
985
views
dittoHeapmap didn't work in my data set(error code :Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds)
dittoseq
scRNAseq
updated 3 days ago by
ATpoint
87k • written 4 days ago by
kayah
▴ 20
1
vote
3
replies
308
views
Visualise duplications and inversions
inversions
duplications
updated 3 days ago by
cmdcolin
★ 4.2k • written 4 days ago by
priya.bmg
▴ 70
1
vote
2
replies
262
views
Exon-level counts via featureCounts
diffSpliceDGE
exon
RNASeq
featureCounts
edgeR
5 hours ago by
n_navy
• 0
0
votes
5
replies
344
views
Picard : Bait_interval and Target_interval
Picard
Bed
read-depth
coverage
updated 3 days ago by
Ram
45k • written 4 days ago by
AIMAR
• 0
3
votes
2
replies
278
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
4 days ago by
lushjia
• 0
0
votes
0
replies
210
views
Question about Calculation of Dietary index in the NHANES Database
index
DI-GM
Dietary
NHANES
5 days ago by
城玮
• 0
0
votes
1
reply
306
views
Detection SNPs and Indels Bacteria
SNPs
updated 5 days ago by
Istvan Albert
102k • written 5 days ago by
Eltercertopico
• 0
1
vote
4
replies
487
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
5 days ago by
Fatemeh
▴ 40
1
vote
3
replies
358
views
Different number of fragments after doublets removal in each run
ArchR
3 days ago by
Bioinformatics_16
• 0
1
vote
2
replies
307
views
Seeking Guidance on Next Steps for DNA Methylation Biomarker Screening in Cancer Prognosis
early-cancer-screening
TCGA
Epigenomics
DNA-Methylation
cancer-prognosis
3 days ago by
Riley J
• 0
0
votes
1
reply
286
views
Help with Panel of Normal (PON)
somatic-mutation
PoN
updated 5 days ago by
Ram
45k • written 5 days ago by
TJ
• 0
9
votes
5
replies
551
views
6 follow
Why don't I see people calculating FPKM from normalized read counts?
normalization
RNA-seq
updated 1 day ago by
kalavattam
▴ 350 • written 6 days ago by
shelkmike
★ 1.5k
1
vote
9
replies
692
views
Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).
EPI2ME
MEDAKA
updated 3 days ago by
GenoMax
150k • written 5 days ago by
Anurag
• 0
0
votes
0
replies
213
views
freebayes with pools of different number of individuals
freebayes
poolseq
5 days ago by
Jeanlain
• 0
0
votes
3
replies
339
views
Insight into Trimmomatic
Trimmomatic
Trimming
Reads
updated 5 days ago by
GenoMax
150k • written 5 days ago by
jh5ym
• 0
1
vote
3
replies
359
views
Trouble when uploading FASTQ files on NCBI
rnaseq
ncbi
4 days ago by
Gerard
▴ 20
1
vote
4
replies
402
views
SyntaxError in file /snakefile, line 22: invalid decimal literal: None
python
snakemake
updated 5 days ago by
Jesse
▴ 870 • written 6 days ago by
Ana
▴ 10
3
votes
2
replies
391
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
6 days ago by
Shravya
• 0
0
votes
0
replies
252
views
News:
Course: Introduction to Genome Annotation (Online, 19–22 May 2025)
Gene-Prediction
Genome-Annotation
Gene-Models
6 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
293
views
Error with running cellranger-atac count
cellranger
atac
single-cell
updated 5 days ago by
Ram
45k • written 6 days ago by
Khôi
• 0
0
votes
2
replies
363
views
HIC-pro with Forward and reverse reads not paired even when I use their test data.
HIC-pro
5 days ago by
Aki
▴ 20
1
vote
1
reply
457
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
updated 6 days ago by
Gordon Smyth
★ 7.9k • written 12 days ago by
Gerard
▴ 20
0
votes
0
replies
311
views
Job:
2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated 6 days ago by
GenoMax
150k • written 6 days ago by
Shicheng Guo
★ 9.6k
1
vote
2
replies
654
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
updated 6 days ago by
GenoMax
150k • written 12 months ago by
Thomas
• 0
4
votes
10
replies
1.0k
views
6 follow
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 6 days ago by
cmdcolin
★ 4.2k • written 17 days ago by
jahnreinhard.ringger
• 0
0
votes
0
replies
282
views
Tutorial:
Fast SCENIC GRN Analysis with RegDiffusion
GRN
network
scRNA-seq
wgcna
7 days ago by
Hao
▴ 10
2
votes
3
replies
808
views
Is it reasonable to do "Gene Regulatory Network Inference" for each cell type and do differential GRN
GRN
scRNA-seq
updated 7 days ago by
Hao
▴ 10 • written 2.6 years ago by
shangguandong1996
▴ 30
1
vote
2
replies
564
views
Blastx issue
blastx
lncRNA
updated 5 days ago by
Ram
45k • written 9 days ago by
Avik
• 0
121,015 results • Page
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Recent Votes
The Biostar Herald for Monday, April 21, 2025
Comment: Why don't I see people calculating FPKM from normalized read counts?
Idat raw data conversion
Idat raw data conversion
A: Illumina BeadArray GTC to VCF conversion
Answer: Analysing gene CNV from TCGA using TCGAbiolinks
Answer: Any recommendation for calculating Fu and Li's D using RStudio?
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Recent Replies
Comment: Deeptools: Custom gcbias plots in R possible?
by
GenoMax
150k
@devon is one of the author's of `deepTools`. His answer in the thread you linked should still be valid. He also warned that the tool was …
Comment: HOMER Motif Analysis-- homer2 error
by
ATpoint
87k
My first approach would always be to run this in native Linux via WSL2. It is probably some cygwin thing that goes away once it is pure Lin…
Comment: HOMER Motif Analysis-- homer2 error
by
Quân
• 0
Hi @HypoGG, I have also encountered the same error. I wonder whether you have found the solution for this matter and will you able to share…
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It?
by
GenoMax
150k
> I'm not working with any lab Unless you are closely working with a lab, it would be difficult to produce a product that would be actual…
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It?
by
Novoo
• 0
I'm not working with any lab , im just a UG biotech student. That's why im having to go on the internet to ask for every little thing.
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It?
by
Novoo
• 0
Oh sorry , I'll keep that in mind.
Comment: ELISA‑Focused Lab Management & Analysis App – Would You Use It?
by
GenoMax
150k
Please do not post similar content in multiple threads: https://www.biostars.org/p/9611446/ You can keep the discussion limited to a singl…
Comment: Exon-level counts via featureCounts
by
n_navy
• 0
When I use -f parameter, Successfully assigned alignments is being extremely low.
Comment: Why don't I see people calculating FPKM from normalized read counts?
by
kalavattam
▴ 350
Thank you for correcting me. I've updated the post.
Comment: miRNA alignment and count generation
by
Jasim
• 0
I am also in the same boat bro, i got 000 countfeauture after aligned. After truobleshooting I found that sam file was failed. My sample wa…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
Mensur Dlakic
★ 29k
My recommendation is to take a couple of days and research what is already available. Is it more productive to spend a week and test severa…
Comment: Running out of disc space with wsl2
by
Mensur Dlakic
★ 29k
I think there is a certain requirement for temporary disk space during prefetch, and you are likely blowing through it by running this in p…
Answer: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Mensur Dlakic
★ 29k
> However, since ML algorithms like KNN, SVM, and NN are sensitive to feature scale and for PCA-based feature extraction, standardization i…
Comment: Why don't I see people calculating FPKM from normalized read counts?
by
dsull
★ 7.4k
Bo Li and Colin Dewey (the developers of RSEM) introduced TPM in 2009 even before the cufflinks paper introduced FPKM. https://academic.oup…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
Novoo
• 0
Thanks so much for the thoughtful feedback—I really appreciate you laying out the practical challenges. Here’s how I’m addressing each of y…
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