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121,022 results • Page
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Tool:
I packaged some tools in python pypi for Windows (fastqc, bowtie2, samtools)
python
pypi
1 hour ago by
Cris
• 0
0
votes
3
replies
199
views
Transcript ID
id
transcript
updated 2 hours ago by
Meeru
• 0 • written 1 day ago by
cheong
• 0
0
votes
1
reply
64
views
Galaxy + RStudio
R
RNA-seq
RStudio
updated 47 minutes ago by
swbarnes2
14k • written 8 hours ago by
justus
• 0
8
votes
18
replies
3.1k
views
8 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 10 hours ago by
jena
▴ 320 • written 19 months ago by
fishingline37
• 0
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 10 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
1
vote
2
replies
138
views
Transcript level quantification and gene length scaling for rRNA depleted libraries
RNASeq
updated 13 hours ago by
dsull
★ 7.4k • written 16 hours ago by
marc.zimmerli
▴ 10
0
votes
0
replies
63
views
Model diagnostics for GAM (Generalised Additive Model)
gam
mgcv
generalized-additive-model
17 hours ago by
Tuấn Anh
• 0
2
votes
5
replies
522
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 17 hours ago by
Darked89
4.7k • written 3 days ago by
Novoo
▴ 10
1
vote
1
reply
132
views
landscape of RNA types and their functions/ scRNA
transcriptomics
scRNA
biology
updated 19 hours ago by
ATpoint
87k • written 21 hours ago by
Ariadna
▴ 20
1
vote
1
reply
108
views
Is vg toolkit suitable for haplotype calling?
pangenome
haplotype
vg
updated 5 hours ago by
Jordan M Eizenga
▴ 700 • written 20 hours ago by
Pau
• 0
0
votes
0
replies
73
views
Dfam annotations
dfam
20 hours ago by
frarodmar17
• 0
0
votes
3
replies
336
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 23 hours ago by
i.sudbery
21k • written 4 days ago by
omicon
▴ 40
1
vote
2
replies
171
views
Cytoscape Node Size Mapping
Cytoscape
1 day ago by
William
▴ 20
1
vote
2
replies
216
views
Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
1 day ago by
RJDan
• 0
0
votes
3
replies
765
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
150
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
1 day ago by
Biostar
3.5k
0
votes
4
replies
223
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
167
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
Cancer-Phylogenetics
Chromosomal-Instability
updated 16 hours ago by
Ram
45k • written 2 days ago by
Bingxin
• 0
1
vote
8
replies
669
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
2 hours ago by
Sib
▴ 60
0
votes
0
replies
170
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
308
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 2 days ago by
Michael
55k • written 5 days ago by
Chatchapon
• 0
1
vote
4
replies
383
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
vladimir_vinarsky
• 0
0
votes
2
replies
254
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
3 days ago by
andrebolerbarros
• 0
0
votes
4
replies
398
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
227
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
5 days ago by
gagi1993
• 0
0
votes
1
reply
281
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
807
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
401
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
22 hours ago by
Matt
• 0
1
vote
3
replies
390
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
388
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
274
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
1.4k
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
372
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
375
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
403
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
336
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
6 days ago by
lushjia
• 0
0
votes
0
replies
264
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
366
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
543
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
6 days ago by
Fatemeh
▴ 40
1
vote
3
replies
422
views
Different number of fragments after doublets removal in each run
ArchR
5 days ago by
Bioinformatics_16
• 0
1
vote
2
replies
366
views
Seeking Guidance on Next Steps for DNA Methylation Biomarker Screening in Cancer Prognosis
early-cancer-screening
TCGA
Epigenomics
DNA-Methylation
cancer-prognosis
5 days ago by
Riley J
• 0
0
votes
1
reply
341
views
Help with Panel of Normal (PON)
somatic-mutation
PoN
updated 6 days ago by
Ram
45k • written 7 days ago by
TJ
• 0
9
votes
5
replies
626
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
771
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
265
views
freebayes with pools of different number of individuals
freebayes
poolseq
7 days ago by
Jeanlain
• 0
0
votes
3
replies
396
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
416
views
Trouble when uploading FASTQ files on NCBI
rnaseq
ncbi
6 days ago by
Gerard
▴ 20
1
vote
4
replies
461
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
446
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
7 days ago by
Shravya
• 0
121,022 results • Page
1 of 2421
Recent Votes
Comment: Is vg toolkit suitable for haplotype calling?
A: Tools To Do the Alternative Splicing Analysis
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
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• 0
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xiaoleiusc
▴ 140
Teacher
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★ 1.3k
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Recent Replies
Comment: Adapter content in FASTQ file
by
xiaoleiusc
▴ 140
I just realized that the adapter sequence depends on the library preparation kit used. For example, our sequencing facility used the Illumi…
Comment: Galaxy + RStudio
by
swbarnes2
14k
Why wouldn't it be possible? The DESeq2 manual has a large section devoted to different ways of importing data in different formats; a plai…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Sib
▴ 60
**No, that’s not correct.** I carefully read your response multiple times (at least 10 times) before formulating my follow-up questions bas…
Comment: Transcript ID
by
Meeru
• 0
Yes, they’re the same. The “-0” is likely just an extra tag from a tool or database, not part of the official Ensembl ID.
Comment: Transcript ID
by
cheong
• 0
Hi ATpoinrt, Thank you! I saw this in the results generated by a software called flair (https://doi.org/10.1038/s41467-020-15171-6) …
Comment: Is vg toolkit suitable for haplotype calling?
by
Jordan M Eizenga
▴ 700
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 …
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