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121,021 results • Page
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0
votes
2
replies
138
views
Transcript ID
id
transcript
just now by
cheong
• 0
0
votes
0
replies
23
views
Galaxy + RStudio
R
RNA-seq
RStudio
2 hours ago by
justus
• 0
8
votes
18
replies
3.0k
views
8 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 4 hours ago by
jena
▴ 320 • written 19 months ago by
fishingline37
• 0
1
vote
2
replies
112
views
Transcript level quantification and gene length scaling for rRNA depleted libraries
RNASeq
updated 7 hours ago by
dsull
★ 7.4k • written 11 hours ago by
marc.zimmerli
▴ 10
0
votes
0
replies
52
views
Model diagnostics for GAM (Generalised Additive Model)
gam
mgcv
generalized-additive-model
11 hours ago by
Tuấn Anh
• 0
2
votes
5
replies
497
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 11 hours ago by
Darked89
4.7k • written 3 days ago by
Novoo
▴ 10
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
1
reply
121
views
landscape of RNA types and their functions/ scRNA
transcriptomics
scRNA
biology
updated 14 hours ago by
ATpoint
87k • written 15 hours ago by
Ariadna
▴ 20
0
votes
1
reply
76
views
Is vg toolkit suitable for haplotype calling?
pangenome
haplotype
vg
updated 30 minutes ago by
Jordan M Eizenga
▴ 690 • written 14 hours ago by
Pau
• 0
0
votes
0
replies
63
views
Dfam annotations
dfam
15 hours ago by
frarodmar17
• 0
0
votes
3
replies
319
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 17 hours ago by
i.sudbery
21k • written 3 days ago by
omicon
▴ 40
1
vote
2
replies
159
views
Cytoscape Node Size Mapping
Cytoscape
1 day ago by
William
▴ 20
1
vote
2
replies
202
views
Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
1 day ago by
RJDan
• 0
0
votes
3
replies
755
views
HOMER Motif Analysis-- homer2 error
rna-seq
homer
updated 1 day ago by
ATpoint
87k • written 15 months ago by
HypoGG
• 0
4
votes
0
replies
139
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
1 day ago by
Biostar
3.5k
0
votes
4
replies
216
views
Forum:
ELISA‑Focused Lab Management & Analysis App – Would You Use It?
biotech
startup
updated 1 day ago by
Ram
45k • written 1 day ago by
Novoo
▴ 10
0
votes
0
replies
157
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
Cancer-Phylogenetics
Chromosomal-Instability
updated 11 hours ago by
Ram
45k • written 2 days ago by
Bingxin
• 0
1
vote
7
replies
629
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
updated 9 hours ago by
Mensur Dlakic
★ 29k • written 3 days ago by
Sib
▴ 60
0
votes
0
replies
163
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 2 days ago by
GenoMax
150k • written 3 days ago by
Abieskawa
• 0
1
vote
1
reply
300
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 2 days ago by
Michael
55k • written 4 days ago by
Chatchapon
• 0
1
vote
4
replies
375
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
247
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
3 days ago by
andrebolerbarros
• 0
0
votes
4
replies
385
views
UCSC's NCBI RefSeq Track tables: header differences
ucsc-genome-browswer
refseq
ncbi
4 days ago by
Synanth
• 0
3
votes
2
replies
1.3k
views
How do you do differential splicing using edgeR command diffSpliceDGE?
differential-splicing
diffSpliceDGE
edger
updated 4 days ago by
Gordon Smyth
★ 7.9k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
218
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
4 days ago by
gagi1993
• 0
0
votes
1
reply
273
views
Issue with Agilent 2100 BioAnalyzer HS DNA Assay Trace
library-preparation
DNA
bioanalyzer
updated 4 days ago by
GenoMax
150k • written 5 days ago by
Beatrice
• 0
1
vote
2
replies
799
views
QIAseq 16S/ITS Screening Panel Primers?
16s
primers
metagenomics
ITS
updated 5 days ago by
GenoMax
150k • written 3.2 years ago by
Isaac
• 0
3
votes
2
replies
387
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
16 hours ago by
Matt
• 0
1
vote
3
replies
381
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
updated 5 days ago by
GenoMax
150k • written 6 days ago by
Sd
• 0
0
votes
0
replies
377
views
Trouble with CIBERSORTx: All P-values > 0.05, Low Correlation, High RMSE – What Could Be Going Wrong?
R
CIBERSORTx
CIBERSORT
script
updated 5 days ago by
GenoMax
150k • written 5 days ago by
Pumla
• 0
0
votes
1
reply
266
views
How can I identify genes with the MSTRG notation?
R
stringtie
RNA-Seq
updated 5 days ago by
GenoMax
150k • written 5 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
1.3k
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 5 days ago by
ATpoint
87k • written 5 days ago by
kayah
▴ 20
1
vote
3
replies
360
views
Visualise duplications and inversions
inversions
duplications
updated 4 days ago by
cmdcolin
★ 4.2k • written 5 days ago by
priya.bmg
▴ 70
1
vote
3
replies
364
views
Exon-level counts via featureCounts
diffSpliceDGE
exon
RNASeq
featureCounts
edgeR
updated 1 day ago by
rfran010
★ 1.4k • written 5 days ago by
n_navy
• 0
0
votes
5
replies
394
views
Picard : Bait_interval and Target_interval
Picard
Bed
read-depth
coverage
updated 5 days ago by
Ram
45k • written 5 days ago by
AIMAR
• 0
3
votes
2
replies
329
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
5 days ago by
lushjia
• 0
0
votes
0
replies
256
views
Question about Calculation of Dietary index in the NHANES Database
index
DI-GM
Dietary
NHANES
6 days ago by
城玮
• 0
0
votes
1
reply
357
views
Detection SNPs and Indels Bacteria
SNPs
updated 6 days ago by
Istvan Albert
102k • written 7 days ago by
Eltercertopico
• 0
1
vote
4
replies
538
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
6 days ago by
Fatemeh
▴ 40
1
vote
3
replies
411
views
Different number of fragments after doublets removal in each run
ArchR
5 days ago by
Bioinformatics_16
• 0
1
vote
2
replies
359
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
332
views
Help with Panel of Normal (PON)
somatic-mutation
PoN
updated 6 days ago by
Ram
45k • written 6 days ago by
TJ
• 0
9
votes
5
replies
619
views
6 follow
Why don't I see people calculating FPKM from normalized read counts?
normalization
RNA-seq
updated 2 days ago by
kalavattam
▴ 350 • written 7 days ago by
shelkmike
★ 1.5k
1
vote
9
replies
757
views
Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).
EPI2ME
MEDAKA
updated 4 days ago by
GenoMax
150k • written 7 days ago by
Anurag
• 0
0
votes
0
replies
258
views
freebayes with pools of different number of individuals
freebayes
poolseq
6 days ago by
Jeanlain
• 0
0
votes
3
replies
390
views
Insight into Trimmomatic
Trimmomatic
Trimming
Reads
updated 7 days ago by
GenoMax
150k • written 7 days ago by
jh5ym
• 0
1
vote
3
replies
410
views
Trouble when uploading FASTQ files on NCBI
rnaseq
ncbi
5 days ago by
Gerard
▴ 20
1
vote
4
replies
453
views
SyntaxError in file /snakefile, line 22: invalid decimal literal: None
python
snakemake
updated 6 days ago by
Jesse
▴ 870 • written 7 days ago by
Ana
▴ 10
3
votes
2
replies
438
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
7 days ago by
Shravya
• 0
0
votes
0
replies
310
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
121,021 results • Page
1 of 2421
Recent Votes
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
A: FRIP score ATAC-seq
A: How to estimate SNP-based heritability?
A: How to estimate SNP-based heritability?
Transcript level quantification and gene length scaling for rRNA depleted libraries
Answer: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
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▴ 140
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Recent Replies
Comment: Is vg toolkit suitable for haplotype calling?
by
Jordan M Eizenga
▴ 690
When you say "extract the haplotypes", are you referring to the read alignments themselves, or do you mean inferring the underlying haploty…
Answer: How to limit fasta header to 40 characters?
by
jena
▴ 320
Looks like a job for [bioawk][1]. For example, if you just need the IDs (like in the seqkit answer above), you can do this: bioawk -c …
Comment: Transcript level quantification and gene length scaling for rRNA depleted librar
by
dsull
★ 7.4k
Haven’t had time to think about this in its entirety but lncRNAs are poorly annotated (in part because their biology is tricky) and TPM len…
Comment: Transcript level quantification and gene length scaling for rRNA depleted librar
by
ATpoint
87k
Interesting observation. Can you add plots to illustrate this? For example for this gene, the salmon output per samples, the tximport resul…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Mensur Dlakic
★ 29k
I have no good idea how to work with data of unknown origin and unknown pre-processing steps. Somehow, you seem to be reading my answers s…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Sib
▴ 60
Unfortunately, I cannot use raw data because I am teaching students who are not yet able to analyze raw data. Instead, we use a series matr…
Answer: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
Darked89
4.7k
I think the best is to strip functionalities to bare essentials: secure storage of the data plus metadata and the backups. For that you may…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
karl.stamm
4.1k
I've seen a few of these posts, and you seem to be highlighting that it is 'lightweight'. I think that's a bad move - what do you think th…
Answer: landscape of RNA types and their functions/ scRNA
by
ATpoint
87k
You are missing the point here. This statement you cite is not about RNA function. What people did there was to add synthetic RNA to the li…
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 prima…
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…
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