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121,016 results • Page
1 of 2421
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0
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miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 1 hour ago by
i.sudbery
21k • written 3 days ago by
omicon
▴ 40
0
votes
1
reply
73
views
Transcript ID
id
transcript
updated just now by
GenoMax
150k • written 7 hours ago by
cheong
• 0
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
1
vote
2
replies
111
views
Cytoscape Node Size Mapping
Cytoscape
16 hours ago by
William
▴ 20
1
vote
2
replies
142
views
Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
17 hours ago by
RJDan
• 0
0
votes
3
replies
720
views
HOMER Motif Analysis-- homer2 error
rna-seq
homer
updated 19 hours ago by
ATpoint
87k • written 15 months ago by
HypoGG
• 0
4
votes
0
replies
103
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
23 hours ago by
Biostar
3.5k
0
votes
4
replies
177
views
Forum:
ELISA‑Focused Lab Management & Analysis App – Would You Use It?
biotech
startup
updated 17 hours ago by
Ram
45k • written 1 day ago by
Novoo
• 0
0
votes
0
replies
123
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
CancerPhylogenetics
ChromosomalInstability
1 day ago by
Bingxin
• 0
1
vote
5
replies
502
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
updated 3 hours ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Sib
▴ 60
0
votes
0
replies
136
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 2 days ago by
GenoMax
150k • written 2 days ago by
Abieskawa
• 0
0
votes
3
replies
380
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 2 days ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Novoo
• 0
1
vote
1
reply
271
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 1 day ago by
Michael
55k • written 4 days ago by
Chatchapon
• 0
1
vote
4
replies
339
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 2 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
vladimir_vinarsky
• 0
0
votes
2
replies
224
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
2 days ago by
andrebolerbarros
• 0
0
votes
4
replies
359
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 3 days ago by
Gordon Smyth
★ 7.9k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
192
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
4 days ago by
gagi1993
• 0
0
votes
1
reply
248
views
Issue with Agilent 2100 BioAnalyzer HS DNA Assay Trace
library-preparation
DNA
bioanalyzer
updated 3 days ago by
GenoMax
150k • written 4 days ago by
Beatrice
• 0
1
vote
2
replies
773
views
QIAseq 16S/ITS Screening Panel Primers?
16s
primers
metagenomics
ITS
updated 4 days ago by
GenoMax
150k • written 3.2 years ago by
Isaac
• 0
3
votes
2
replies
326
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
21 minutes ago by
Matt
• 0
1
vote
3
replies
355
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
updated 4 days ago by
GenoMax
150k • written 5 days ago by
Sd
• 0
0
votes
0
replies
335
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
241
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
1.1k
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 4 days ago by
ATpoint
87k • written 4 days ago by
kayah
▴ 20
1
vote
3
replies
336
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
3
replies
325
views
Exon-level counts via featureCounts
diffSpliceDGE
exon
RNASeq
featureCounts
edgeR
updated 16 hours ago by
rfran010
★ 1.4k • written 4 days ago by
n_navy
• 0
0
votes
5
replies
369
views
Picard : Bait_interval and Target_interval
Picard
Bed
read-depth
coverage
updated 4 days ago by
Ram
45k • written 5 days ago by
AIMAR
• 0
3
votes
2
replies
304
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
5 days ago by
lushjia
• 0
0
votes
0
replies
232
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
331
views
Detection SNPs and Indels Bacteria
SNPs
updated 5 days ago by
Istvan Albert
102k • written 6 days ago by
Eltercertopico
• 0
1
vote
4
replies
509
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
5 days ago by
Fatemeh
▴ 40
1
vote
3
replies
387
views
Different number of fragments after doublets removal in each run
ArchR
4 days ago by
Bioinformatics_16
• 0
1
vote
2
replies
333
views
Seeking Guidance on Next Steps for DNA Methylation Biomarker Screening in Cancer Prognosis
early-cancer-screening
TCGA
Epigenomics
DNA-Methylation
cancer-prognosis
4 days ago by
Riley J
• 0
0
votes
1
reply
308
views
Help with Panel of Normal (PON)
somatic-mutation
PoN
updated 5 days ago by
Ram
45k • written 6 days ago by
TJ
• 0
9
votes
5
replies
588
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
724
views
Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).
EPI2ME
MEDAKA
updated 3 days ago by
GenoMax
150k • written 6 days ago by
Anurag
• 0
0
votes
0
replies
235
views
freebayes with pools of different number of individuals
freebayes
poolseq
6 days ago by
Jeanlain
• 0
0
votes
3
replies
363
views
Insight into Trimmomatic
Trimmomatic
Trimming
Reads
updated 6 days ago by
GenoMax
150k • written 6 days ago by
jh5ym
• 0
1
vote
3
replies
382
views
Trouble when uploading FASTQ files on NCBI
rnaseq
ncbi
5 days ago by
Gerard
▴ 20
1
vote
4
replies
426
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
413
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
6 days ago by
Shravya
• 0
0
votes
0
replies
283
views
News:
Course: Introduction to Genome Annotation (Online, 19–22 May 2025)
Gene-Prediction
Genome-Annotation
Gene-Models
7 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
315
views
Error with running cellranger-atac count
cellranger
atac
single-cell
updated 6 days ago by
Ram
45k • written 7 days ago by
Khôi
• 0
0
votes
2
replies
386
views
HIC-pro with Forward and reverse reads not paired even when I use their test data.
HIC-pro
6 days ago by
Aki
▴ 20
1
vote
1
reply
480
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
updated 7 days ago by
Gordon Smyth
★ 7.9k • written 12 days ago by
Gerard
▴ 20
0
votes
0
replies
335
views
Job:
2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated 7 days ago by
GenoMax
150k • written 7 days ago by
Shicheng Guo
★ 9.6k
1
vote
2
replies
677
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
updated 7 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 7 days ago by
cmdcolin
★ 4.2k • written 17 days ago by
jahnreinhard.ringger
• 0
0
votes
0
replies
305
views
Tutorial:
Fast SCENIC GRN Analysis with RegDiffusion
GRN
network
scRNA-seq
wgcna
7 days ago by
Hao
▴ 10
121,016 results • Page
1 of 2421
Recent Votes
The Biostar Herald for Monday, April 21, 2025
Answer: Analysing gene CNV from TCGA using TCGAbiolinks
Differential methylation rate analysis using modkit for m6A
Comment: Differential methylation rate analysis using modkit for m6A
C: Mapping sequencing reads to 5-UTR, 3-UTR and CDS using Ensembl GTF files
C: Mapping sequencing reads to 5-UTR, 3-UTR and CDS using Ensembl GTF files
Mapping sequencing reads to 5-UTR, 3-UTR and CDS using Ensembl GTF files
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Recent Replies
Answer: miRNA alignment and count generation
by
i.sudbery
21k
If you are aligning to a transcriptome based index (like the mature or hairpin fasta files), then you don't need a gff. The gff tells read …
Comment: Analysing gene CNV from TCGA using TCGAbiolinks
by
Matt
• 0
Great, thank you, that's very helpful. It seems if I filter to only query the 'primary tumour' samples from GDC all the samples use the ABS…
Comment: bbsplit : How to configure ambiguous/ambiguous2 parameters in order to consider
by
ZheFrench
▴ 590
#name %unambiguousReads unambiguousMB %ambiguousReads ambiguousMB unambiguousReads ambiguousReads assignedReads assignedBases primary 99.59…
Answer: miRNA alignment and count generation
by
Barry Digby
★ 1.3k
Align to the hairpins, not the mature miRNA file. This should get you started preparing a `hsa` hairpin file. If your species differs, …
Comment: Transcript ID
by
ATpoint
87k
Hi, yes ENS*G* is gene and *T* is transcript. The `-0` is (to me knowledge) no Ensembl standard so it is probably custom. Maybe some contex…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Mensur Dlakic
★ 29k
I do data normalization almost on a daily basis, but not with this type of data. There could be a more useful advice coming from someone wh…
Answer: Cytoscape Node Size Mapping
by
William
▴ 20
Oh - I figured it out. Have to set Lock Node Width and Height, and also Fit custom graphic to node.
Comment: Exon-level counts via featureCounts
by
rfran010
★ 1.4k
Perhaps you have not also allowed multi-overlapping? (exons from different transcripts of the same gene will overlap each other)
Comment: Deeptools: Custom gcbias plots in R possible?
by
RJDan
• 0
Thanks. I'm looking into using picard.
Comment: Cytoscape Node Size Mapping
by
William
▴ 20
Strangely - if I make my own style, it is grayed out, but if click "solid" style - I can set the size.
Comment: fgsea tutorial issue with BiocParallel
by
cwwong13
▴ 40
I encountered the same error even with recent installs (R4.4.2/fgsea_1.32.2/BiocParallel_1.40.0). May I know if there are any workarounds t…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Sib
▴ 60
Thank you for the detailed explanation. You mentioned that `[-10, 10]` is a large range. Initially, my data spanned `[-6, 17]`. After **qua…
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…
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