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121,576 results • Page
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0
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11
views
Two config files for one Snakemake file
config
yaml
snakemake
43 minutes ago by
Xiaokang
▴ 80
6
votes
5
replies
10k
views
TCGA MSI status
TCGA
clinical
MSI
updated 7 hours ago by
GenoMax
152k • written 8.7 years ago by
jan
▴ 170
0
votes
1
reply
96
views
Summing the counts of duplicated genes in RNA seq data?
genes
Duplicated
updated 12 hours ago by
GenoMax
152k • written 12 hours ago by
toobavaraste
• 0
1
vote
0
replies
65
views
Assembling a derivative chromosome from ONT WGS data
ONT
assembly
Whole-Genome
13 hours ago by
Noah
▴ 20
843
votes
170
replies
182k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 11 weeks ago by
Biostar
3.6k • written 8.6 years ago by
Istvan Albert
102k
2
votes
5
replies
170
views
[VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
vg
13 hours ago by
saruman
• 0
0
votes
8
replies
285
views
Strandedness issues in STAR quantification
STAR
stranded
updated 15 hours ago by
GenoMax
152k • written 18 hours ago by
marek.gierlinski
• 0
0
votes
1
reply
111
views
naccess installation error
naccess
updated 16 hours ago by
GenoMax
152k • written 19 hours ago by
Angelo
• 0
1
vote
2
replies
761
views
Download Isoform expression data from tcga
cancer
transcript
gene
isoform
updated 13 hours ago by
GenoMax
152k • written 2.7 years ago by
nourmahfel
▴ 10
6
votes
11
replies
3.3k
views
Visualization of RNA-seq gene expression only one gene of interest between 2 conditions
RNA-seq
updated 21 hours ago by
rajdeepboral00
▴ 70 • written 21 months ago by
Chris
▴ 360
2
votes
2
replies
147
views
Exome data analysis computing resources requirement query
exome
updated 17 hours ago by
GenoMax
152k • written 22 hours ago by
1769mkc
★ 1.3k
0
votes
1
reply
100
views
feature_ref files in upstream analyses related to Perturb-seq
perturb-seq
updated 12 hours ago by
GenoMax
152k • written 22 hours ago by
2443422660
• 0
1
vote
2
replies
146
views
Splitting chromosomes into contigs within BAM and GTF files
samtools
gtf
chromosome
annotation
bam
19 hours ago by
MAB
• 0
5
votes
7
replies
392
views
Forum:
Theoretical Question: Is Sub-Angstrom Geometric Identity (RMSD < 0.1 Å) in Convergent Evolution Possible?
Kinesin
Biophysics
Biology
Molecular
Myosin
updated 15 hours ago by
GenoMax
152k • written 1 day ago by
Alberto
▴ 10
0
votes
0
replies
88
views
News:
online course: An Introduction to Nanopore Direct RNA Sequencing (RNA004) - 27–30 October
DirectRNAseq
Nanopore
RNA004
RNAModifications
1 day ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
158
views
Refflat file for Rattus norvegicus
file
RefFlat
Rattus
RNA-seq
norvegicus
updated 1 day ago by
GenoMax
152k • written 1 day ago by
AIMAR
▴ 50
2
votes
6
replies
322
views
Forum:
LogFC on geometric means vs on arithmetic means. Presto vs Seurat
Presto
Seurat
logFC
general
questions
updated 16 hours ago by
ATpoint
88k • written 1 day ago by
e.r.zakiev
▴ 260
1
vote
1
reply
424
views
Question about anova-like test using Limma
makeContrasts
limma
updated 1 day ago by
Gordon Smyth
★ 8.2k • written 13 months ago by
Daniel
▴ 10
5
votes
3
replies
289
views
asking for optimized bash scripting
analysis
updated 19 hours ago by
Joe
22k • written 1 day ago by
QX
▴ 80
0
votes
5
replies
288
views
Differential expression genes
SEQ
DGE
RNA
updated 17 hours ago by
GenoMax
152k • written 1 day ago by
m90
▴ 30
2
votes
3
replies
271
views
Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Length in ChIP-seq Dataset
macs3
15 hours ago by
christoph.neu
▴ 10
3
votes
4
replies
258
views
Plotting of genes using tpm matrix
normalization
TPM
boxplot
updated 12 hours ago by
i.sudbery
21k • written 1 day ago by
rajdeepboral00
▴ 70
3
votes
2
replies
227
views
A question about model matrix and contrast
makeContrasts
limma
1 day ago by
jkim
▴ 210
0
votes
1
reply
341
views
Understanding MAG completeness and contig composition in metagenomic bins
data
shotgun
updated 1 day ago by
andres.firrincieli
3.9k • written 6 days ago by
shevch2009
▴ 20
2
votes
4
replies
316
views
Understanding NCBI vs ENA data
ENA
NCBI
SRA
updated 1 day ago by
GenoMax
152k • written 3 days ago by
wes
▴ 90
0
votes
2
replies
218
views
Job:
Assistance running population specific hapibd
ancestry
haplotype
IBD
updated 2 days ago by
cmdcolin
★ 4.3k • written 2 days ago by
CJ169
• 0
2
votes
1
reply
171
views
Empty result using enrichGO
clusterProfiler
updated 2 days ago by
GenoMax
152k • written 2 days ago by
Chris
▴ 360
2
votes
1
reply
5.7k
views
Convert ct file to dot bracket format
RNA
structure
updated 2 days ago by
zahraniasari.2023
• 0 • written 8.6 years ago by
abdullahrenk
▴ 30
0
votes
2
replies
1.0k
views
News:
Hands-On Workshop - Next-Generation Sequencing Data Analysis: A Practical Introduction (September 10-12, 2025 in Berlin, Germany)
Workshop
RNA-Seq
Illumina
VariantCalling
DNA-Seq
2 days ago by
ecSeq Bioinformatics
▴ 20
0
votes
0
replies
122
views
Is it possible to perform XP-EHH and iHS on targeted sequencing data without a .map file?
ngs
ihs
analysis
selection
sequencing
2 days ago by
slzr_
▴ 10
0
votes
1
reply
171
views
Discrepancy in RNA editing calls between STAR and Subjunc aligners using JACUSA2
jacusa2
rnaseq
subjunc
star
rsubread
updated 21 hours ago by
Mark
★ 1.7k • written 2 days ago by
thomas.heigl.ibk
• 0
2
votes
1
reply
186
views
RNA-Seq paired-end datasets
paired-end
RNA-seq
Bioinformatic
updated 2 days ago by
Matthias Zepper
5.1k • written 2 days ago by
AIMAR
▴ 50
0
votes
0
replies
171
views
News:
Course: Introduction to CRISPR
GenomeEditing
CRISPR
Evolution
3 days ago by
Physalia-courses
★ 2.6k
2
votes
3
replies
474
views
Best strategy for comparing cell-type composition between disease and healthy groups in single-cell RNA-seq data
Single_cell
updated 1 day ago by
ATpoint
88k • written 3 days ago by
城玮
• 0
1
vote
4
replies
328
views
RNA-seq assigned alignments
paired-end
STAR
RNA-seq
mapping
single-end
updated 3 days ago by
jaro.slamecka
▴ 270 • written 3 days ago by
Manko47
▴ 10
0
votes
1
reply
244
views
Obtain Common SNPS for Mouse Genome
mouse
SNPs
updated 3 days ago by
GenoMax
152k • written 3 days ago by
joe_genome
▴ 60
1
vote
3
replies
411
views
How do you clean GEO metadata before downstream analysis?
geo
updated 3 days ago by
yura.grabovska
▴ 800 • written 5 days ago by
Alba
• 0
0
votes
1
reply
245
views
Seeking high-quality curated metabolic models with time-resolved flux data for sonification project
metabolism
sonification
networks
updated 4 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
omereilam1
• 0
0
votes
0
replies
189
views
Standard way to represent represent indel (insertion or deletion) alleles within a haplotype
haplotypes
indels
haploview
4 days ago by
Mwangana
• 0
1
vote
1
reply
309
views
lovis4u Configuration
graph
lovis4u
genomics
updated 4 days ago by
GenoMax
152k • written 5 days ago by
NIkita
• 0
1
vote
1
reply
344
views
Tool:
Tool to clean GEO metadata
GEO
metadata
updated 3 days ago by
yura.grabovska
▴ 800 • written 5 days ago by
Alba
• 0
1
vote
2
replies
601
views
WGBS Analysis with 1 control sample and 6 disease samples
one
WGBS
sample
updated 4 days ago by
ATpoint
88k • written 16 days ago by
Cassandra
▴ 10
0
votes
2
replies
606
views
How to extract gene list from GEO dataset in R
coding
beginner
question
r
updated 5 days ago by
Shohel
• 0 • written 16 days ago by
decorus
• 0
2
votes
6
replies
592
views
RNA seq strandedness (reverse-strand)
seq
reverse-stranded
strand
RNA
4 days ago by
ZuelTech
• 0
0
votes
0
replies
249
views
TFs and enrichment analysis for TRAP sequencing
TRAP
6 days ago by
Genesis
• 0
0
votes
2
replies
363
views
Extract track data from "search by region" feature on ENCODE
Encode
3 days ago by
AlienPumpkinPie
• 0
9
votes
8
replies
1.0k
views
Weird p-value distribution on edgeR results
edgeR
pvalue-distribution
gene-expression
updated 6 days ago by
dariober
15k • written 14 days ago by
Guillermo
▴ 30
1
vote
3
replies
401
views
Draw GO tree for some GO ids with coloring
enrichment
GO
6 days ago by
boczniak767
▴ 880
2
votes
4
replies
2.7k
views
Extract transcript fasta using gff
fasta
gff
updated 6 days ago by
cmdcolin
★ 4.3k • written 4.1 years ago by
boczniak767
▴ 880
1
vote
4
replies
1.2k
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
updated 6 days ago by
Jasim
• 0 • written 15 months ago by
otieno43
▴ 40
121,576 results • Page
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Assembling a derivative chromosome from ONT WGS data
Comment: LogFC on geometric means vs on arithmetic means. Presto vs Seurat
Answer: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
Answer: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
Comment: Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Leng
Comment: Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Leng
Answer: asking for optimized bash scripting
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Recent Replies
Comment: TCGA MSI status
by
GenoMax
152k
You can get some data from GDC portal: https://portal.gdc.cancer.gov/analysis_page?app= and https://portal.gdc.cancer.gov/analysis_page?app…
Comment: TCGA MSI status
by
Muhammad Rohan Ali
• 0
Can I get TCGA somatic mutation vcf files or maf files for MSI - H, MSI-L - MSS samples? I mean open access without any special access…
Comment: feature_ref files in upstream analyses related to Perturb-seq
by
GenoMax
152k
What kind of technology is this data from? If it is Parse tech data then you may need to use their pipeline that you can get from here: htt…
Comment: Summing the counts of duplicated genes in RNA seq data?
by
GenoMax
152k
> duplicated genes What is the origin of those genes. Are they entries with same name in GTF but different chromosomal locations (e.g. cop…
Comment: Plotting of genes using tpm matrix
by
i.sudbery
21k
Yes, the y-axis is reasonable. ALthough the test for differences should come from DESeq, rather than from a wilcox in this case. With four …
Comment: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
by
saruman
• 0
Done. Thank you.
Comment: Download Isoform expression data from tcga
by
GenoMax
152k
Far as I know TCGA did not do transcript level expression as a standard analysis (see the list here --> https://docs.gdc.cancer.gov/Data/Bi…
Comment: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
by
GenoMax
152k
https://www.biostars.org/u/45375/ : Please accept this answer (green check mark) to provide closure for this thread.
Comment: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
by
saruman
• 0
And thank you for the great work!
Comment: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
by
saruman
• 0
Thank you so much. I did not fully grasp the `vg gbwt` command.
Answer: [VG sim, surject, giraffe] How to remove a sample from GFA/GBZ graph
by
Jouni Sirén
▴ 710
You can remove a sample from a GBZ graph in two steps. First you extract the GBWT index from the GBZ file: ``` vg gbwt -o graph.gbwt -Z…
Comment: Strandedness issues in STAR quantification
by
GenoMax
152k
Since the program author has recommended it, can you try indexing without the GTF and then counting again. You don't have polycistronic tra…
Comment: Theoretical Question: Is Sub-Angstrom Geometric Identity (RMSD < 0.1 Å) in Conve
by
GenoMax
152k
Monellin and Thaumatin are of significantly different size and show no sequence homology. They have completely different tertiary structure…
Comment: Strandedness issues in STAR quantification
by
marek.gierlinski
• 0
Oh, I wouldn't know what to look for in IGV. The issue is with quantification, and looking at a BAM file in IGV does not tell me how a give…
Comment: Discrepancy Between Fragment Size Distribution and MACS3-Predicted Fragment Leng
by
christoph.neu
▴ 10
The Bioanalyzer was used to check if a library preparation would be worth it, that's why we did it before hand. And I was expecting a bit o…
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