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121,030 results • Page
1 of 2421
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how to handle infinite M-values in methylation array data
M-value
methylation
infinite
array
33 minutes ago by
matt192
• 0
1
vote
3
replies
544
views
Snakemake - pipeline shut down without error
snakemake
1 hour ago by
bhumm
▴ 200
0
votes
1
reply
54
views
Source for `transcript_name` in GTFs
GTF
updated 2 hours ago by
GenoMax
150k • written 4 hours ago by
gernophil
▴ 120
5
votes
5
replies
188
views
Tool:
Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and de-duplication using cutadapt
rad-seq
ddRADseq
demultiplexing
deduplication
5 hours ago by
Rafal
▴ 10
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
0
votes
2
replies
68
views
How to normalised DNA sequencing depth for genomic variant discovery ?
normalisation
read-depth
variant-calling
updated 4 hours ago by
Ram
45k • written 6 hours ago by
AIMAR
• 0
2
votes
4
replies
150
views
RNASeq featureCounts Help Needed
fungi
featurecounts
RNASeq
5 hours ago by
SomeOne
▴ 170
0
votes
0
replies
57
views
PAUP* error with exporting result file
PAUP
SVDquartet
7 hours ago by
ylkim9
• 0
0
votes
1
reply
70
views
I need to convert Axiom output to PLINK format I did not find annotation.db
Axiom
PLINK
apt-format-result
updated 5 hours ago by
GenoMax
150k • written 8 hours ago by
AlmuhayyaA
• 0
0
votes
1
reply
94
views
How to merge heterogeneously normalized RNA-seq datasets for meta-analysis?
normalization
rna-seq
updated 7 hours ago by
ATpoint
87k • written 10 hours ago by
pipelinfections
• 0
0
votes
0
replies
70
views
Tool:
I packaged some tools in python pypi for Windows (fastqc, bowtie2, samtools)
python
pypi
12 hours ago by
Cris
• 0
0
votes
3
replies
242
views
Transcript ID
id
transcript
updated 13 hours ago by
Meeru
• 0 • written 1 day ago by
cheong
• 0
0
votes
1
reply
111
views
Galaxy + RStudio
R
RNA-seq
RStudio
updated 11 hours ago by
swbarnes2
14k • written 19 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 21 hours ago by
jena
▴ 320 • written 19 months ago by
fishingline37
• 0
1
vote
2
replies
167
views
Transcript level quantification and gene length scaling for rRNA depleted libraries
RNASeq
updated 1 day ago by
dsull
★ 7.4k • written 1 day ago by
marc.zimmerli
▴ 10
0
votes
0
replies
87
views
Model diagnostics for GAM (Generalised Additive Model)
gam
mgcv
generalized-additive-model
1 day ago by
Tuấn Anh
• 0
2
votes
5
replies
558
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 1 day ago by
Darked89
4.7k • written 4 days ago by
Novoo
▴ 10
1
vote
1
reply
150
views
landscape of RNA types and their functions/ scRNA
transcriptomics
scRNA
biology
updated 1 day ago by
ATpoint
87k • written 1 day ago by
Ariadna
▴ 20
1
vote
1
reply
133
views
Is vg toolkit suitable for haplotype calling?
pangenome
haplotype
vg
updated 16 hours ago by
Jordan M Eizenga
▴ 700 • written 1 day ago by
Pau
• 0
0
votes
0
replies
91
views
Dfam annotations
dfam
1 day ago by
frarodmar17
• 0
0
votes
3
replies
357
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 1 day ago by
i.sudbery
21k • written 4 days ago by
omicon
▴ 40
1
vote
2
replies
191
views
Cytoscape Node Size Mapping
Cytoscape
2 days ago by
William
▴ 20
1
vote
2
replies
235
views
Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
2 days ago by
RJDan
• 0
0
votes
3
replies
783
views
HOMER Motif Analysis-- homer2 error
rna-seq
homer
updated 2 days ago by
ATpoint
87k • written 15 months ago by
HypoGG
• 0
4
votes
0
replies
168
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
2 days ago by
Biostar
3.5k
0
votes
4
replies
243
views
Forum:
ELISA‑Focused Lab Management & Analysis App – Would You Use It?
biotech
startup
updated 2 days ago by
Ram
45k • written 2 days ago by
Novoo
▴ 10
0
votes
0
replies
189
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
Cancer-Phylogenetics
Chromosomal-Instability
updated 1 day ago by
Ram
45k • written 2 days ago by
Bingxin
• 0
1
vote
10
replies
779
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
updated 4 hours ago by
Mensur Dlakic
★ 29k • written 4 days ago by
Sib
▴ 60
0
votes
0
replies
186
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 3 days ago by
GenoMax
150k • written 3 days ago by
Abieskawa
• 0
1
vote
1
reply
325
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
409
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 3 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
vladimir_vinarsky
• 0
0
votes
2
replies
274
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
3 days ago by
andrebolerbarros
• 0
0
votes
4
replies
418
views
UCSC's NCBI RefSeq Track tables: header differences
ucsc-genome-browswer
refseq
ncbi
5 days ago by
Synanth
• 0
3
votes
2
replies
1.4k
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
243
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
5 days ago by
gagi1993
• 0
0
votes
1
reply
299
views
Issue with Agilent 2100 BioAnalyzer HS DNA Assay Trace
library-preparation
DNA
bioanalyzer
updated 5 days ago by
GenoMax
150k • written 6 days ago by
Beatrice
• 0
1
vote
2
replies
824
views
QIAseq 16S/ITS Screening Panel Primers?
16s
primers
metagenomics
ITS
updated 6 days ago by
GenoMax
150k • written 3.2 years ago by
Isaac
• 0
3
votes
2
replies
421
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
1 day ago by
Matt
• 0
1
vote
3
replies
409
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
updated 6 days ago by
GenoMax
150k • written 6 days ago by
Sd
• 0
0
votes
0
replies
421
views
Trouble with CIBERSORTx: All P-values > 0.05, Low Correlation, High RMSE – What Could Be Going Wrong?
R
CIBERSORTx
CIBERSORT
script
updated 6 days ago by
GenoMax
150k • written 6 days ago by
Pumla
• 0
0
votes
1
reply
294
views
How can I identify genes with the MSTRG notation?
R
stringtie
RNA-Seq
updated 6 days ago by
GenoMax
150k • written 6 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
1.5k
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 6 days ago by
ATpoint
87k • written 6 days ago by
kayah
▴ 20
1
vote
3
replies
390
views
Visualise duplications and inversions
inversions
duplications
updated 5 days ago by
cmdcolin
★ 4.2k • written 6 days ago by
priya.bmg
▴ 70
1
vote
3
replies
397
views
Exon-level counts via featureCounts
diffSpliceDGE
exon
RNASeq
featureCounts
edgeR
updated 2 days ago by
rfran010
★ 1.4k • written 6 days ago by
n_navy
• 0
0
votes
5
replies
425
views
Picard : Bait_interval and Target_interval
Picard
Bed
read-depth
coverage
updated 5 days ago by
Ram
45k • written 6 days ago by
AIMAR
• 0
3
votes
2
replies
352
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
6 days ago by
lushjia
• 0
0
votes
0
replies
279
views
Question about Calculation of Dietary index in the NHANES Database
index
DI-GM
Dietary
NHANES
7 days ago by
城玮
• 0
0
votes
1
reply
383
views
Detection SNPs and Indels Bacteria
SNPs
updated 7 days ago by
Istvan Albert
102k • written 7 days ago by
Eltercertopico
• 0
1
vote
4
replies
560
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
7 days ago by
Fatemeh
▴ 40
1
vote
3
replies
439
views
Different number of fragments after doublets removal in each run
ArchR
5 days ago by
Bioinformatics_16
• 0
121,030 results • Page
1 of 2421
Recent Votes
Answer: Snakemake - pipeline shut down without error
Answer: Getting sequences from fastq file using Grep command
Comment: RNASeq featureCounts Help Needed
Comment: RNASeq featureCounts Help Needed
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
A: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
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Answer: Snakemake - pipeline shut down without error
by
bhumm
▴ 200
Circling back to answer my own question. After testing the `--dry-run` (as @Shred suggested) it completed as expected. The rule that consis…
Answer: Source for `transcript_name` in GTFs
by
GenoMax
150k
Manual annotation is done by `HAVANA` group from Ensembl: https://www.ensembl.org/info/genome/genebuild/manual_havana.html It would be fair…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Mensur Dlakic
★ 29k
> Additionally, I’d greatly appreciate your insights on how to handle this issue for KNN, PCA, and Relief? I again refer you to what I alr…
Comment: What is the best way to know if a pair of genes is random?
by
shelkmike
★ 1.5k
Have you tried using the percentile in the distribution of Jaccard indices as the metric of randomness, as I suggested?
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
by
Rafal
▴ 10
@atpoint dependencies and hardcoding taken care of for the moment. Thanks again!
Comment: RNASeq featureCounts Help Needed
by
SomeOne
▴ 170
It was relly helpfull. Thank You.
Comment: How to normalised DNA sequencing depth for genomic variant discovery ?
by
AIMAR
• 0
Aaah I didn't know about that, could you share any document that mention that cause it'll be helpfull. Also the thing I've normal samples a…
Comment: How to normalised DNA sequencing depth for genomic variant discovery ?
by
zizigolu
★ 4.3k
You don’t need to manually normalize read depth before variant calling. Most somatic variant callers (like Mutect2, Strelka2, VarScan2) alr…
Comment: What is the best way to know if a pair of genes is random?
by
Ana
▴ 10
Coming back to this... I am having some trouble because, as I expected, when I obtain the overlap of GO terms in a given pair of genes and …
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
by
Rafal
▴ 10
Right! It is ready in ddradseq_pre.bash but in ddradseq_dedup.bash command line variables setup is not working yet. The directory variable…
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
by
ATpoint
87k
> The variables can be set in command line, also directory Is it? Looks hardcoded to me: https://github.com/rafalwoycicki/ddRADseq_reads/b…
Comment: RNASeq featureCounts Help Needed
by
GenoMax
150k
See answers here for question #3: https://support.bioconductor.org/p/78975/ and also https://support.bioconductor.org/p/9147887/#9147987 Y…
Comment: RNASeq featureCounts Help Needed
by
SomeOne
▴ 170
Hi. @genomax thank you for responding. 1. mRNA data is short read illumina. 2. NP02_scf_1 is scaffold name in my genome.fasta and ge…
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
by
Rafal
▴ 10
Thank you @atpoint for your feedback. I will try to add some safety measures, and thanks for the zcat info. I will try to list the dependie…
Comment: I need to convert Axiom output to PLINK format I did not find annotation.db
by
GenoMax
150k
> apt-genotype-axiom Curious as to what software package are you using here? That beginning `apt` sounds like package manager command fro…
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