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120,143 results • Page
1 of 2403
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ChromHMM - annotation of chromatin states
state
Annoation
18 minutes ago by
Bioinformatics_16
• 0
0
votes
1
reply
43
views
How to trim sequences
trimming
sequencing
phylogenetics
updated 1 hour ago by
Mensur Dlakic
★ 28k • written 3 hours ago by
PF
• 0
0
votes
0
replies
34
views
Use of Pval v.s. Padj Statistic in Pre-Ranked GSEA Analysis
Gene
Ontology
GSEA
RNA-Seq
3 hours ago by
BioTinker
• 0
825
votes
169
replies
164k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.3k • written 8.1 years ago by
Istvan Albert
102k
0
votes
0
replies
35
views
Job:
Postdoctoral Fellow (Quantitative Modeling Group)
Bioengineering
Computational-Biology
updated 3 hours ago by
Ram
44k • written 4 hours ago by
BerkeleyLab
▴ 70
0
votes
1
reply
62
views
How to download metadata for the Broad Firehose RNA-seq data?
metadata
tcga
rnaseq
updated 4 hours ago by
GenoMax
148k • written 6 hours ago by
mebius_band
• 0
0
votes
3
replies
270
views
Interpreting Varied Survival Times in TCGA-BRCA Data
Survival
Kaplan-Meier
TCGA
analysis
survival
curves
updated 6 hours ago by
mebius_band
• 0 • written 14 days ago by
Siqi
• 0
1
vote
2
replies
364
views
Web- based bioinformatics tool/s for identification of cysteine-rich proteins
cysteine
proteins
updated 7 hours ago by
Mensur Dlakic
★ 28k • written 5 months ago by
lukhanyomakhabane
▴ 30
0
votes
1
reply
75
views
Reducing runtime of low-score alignments
python
pairwise-alignment
alignment
updated 8 hours ago by
Mensur Dlakic
★ 28k • written 8 hours ago by
benjlishani7
• 0
3
votes
8
replies
181
views
constructing de novo assembly of plant short reads
short
reads
assembly
plants
updated 9 hours ago by
Dave Carlson
★ 2.1k • written 9 hours ago by
analyst
▴ 50
0
votes
0
replies
55
views
News:
Course live online Intro Bayesian Analysis, February 17th-21st, 2025
python
bayesian
rproject
statistics
12 hours ago by
Sole
• 0
1
vote
0
replies
72
views
Herald:
The Biostar Herald for Tuesday, January 21, 2025
herald
12 hours ago by
Biostar
3.3k
2
votes
3
replies
139
views
Discover novel transcripts
transcriptomic
assembly
stringtie
stringtie--merge
updated 12 hours ago by
lieven.sterck
15k • written 14 hours ago by
Emy Alade
• 0
1
vote
1
reply
99
views
Creating pangenome graphs using vcf files?
pangenome
updated 11 hours ago by
GenoMax
148k • written 14 hours ago by
Uveyik
▴ 60
0
votes
0
replies
87
views
News:
Computational Pangenomics course
Pangenomics
Pangenome-Graphs
18 hours ago by
Physalia-courses
★ 2.6k
1
vote
3
replies
142
views
gene annotation tool recommendations for oomycetes
oomycetes
annotation
updated 7 hours ago by
GenoMax
148k • written 19 hours ago by
colindaven
7.0k
19
votes
10
replies
581
views
7 follow
STAR aligner - Is this still maintained?
STAR
aligner
rnaseq
17 hours ago by
Joshi
• 0
0
votes
4
replies
621
views
Does anyone know how to transform the following transcript ID's from TCGA isoform data
UCSC
isoform
TCGA
updated 21 hours ago by
Zhenyu Zhang
★ 1.2k • written 25 days ago by
B.N.
▴ 10
0
votes
0
replies
71
views
eQTL Analysis for Structural Variants (SV) – Seeking Relevant Software
eQTL
SV
22 hours ago by
chiyong4783
• 0
0
votes
1
reply
110
views
SRA fastq modify by 10x valid fastq
fastq
updated 1 day ago by
GenoMax
148k • written 1 day ago by
wyuan37
• 0
0
votes
1
reply
107
views
Building pangenome graphs in minigraph-cactus using vcf?
pangenome
vcf
cactus
updated 21 hours ago by
Mark
★ 1.6k • written 1 day ago by
Uveyik
▴ 60
0
votes
2
replies
171
views
RSEM and STAR
STAR
RNASeq
RSEM
1 day ago by
rajdeepboral00
▴ 20
0
votes
0
replies
92
views
Interpretaion of tensorQTL output for ieQTL analysis
TensorQTL
IeQTL
Beta-Values
updated 1 day ago by
Ram
44k • written 1 day ago by
cool.aditya286
• 0
4
votes
10
replies
4.5k
views
6 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 1 day ago by
GenoMax
148k • written 4 months ago by
Martina
• 0
1
vote
3
replies
212
views
How to compare gene prediction
gene-prediction
updated 7 hours ago by
Mensur Dlakic
★ 28k • written 1 day ago by
Acervo
• 0
0
votes
0
replies
105
views
ArchR extending gene activity till nearest promoter
ArchR
addGeneScoreMat
1 day ago by
Bastien Hervé
6.1k
0
votes
0
replies
108
views
Heritability
greml
heritability
1 day ago by
am29
▴ 50
0
votes
1
reply
148
views
Transcriptome Reconstruction for Transcript Discovery
taco
stringtie
updated 20 hours ago by
michael.ante
★ 3.9k • written 1 day ago by
Emy Alade
• 0
2
votes
2
replies
193
views
Having trouble running Desktop version of Pse-in-One
Pse-in-One
DNA
22 hours ago by
Jimmy
▴ 30
0
votes
0
replies
106
views
Comparison of different gene catalog abundance
assembly
catalog
metagenome
illumina
gene
1 day ago by
young_bioinformatician
▴ 240
0
votes
1
reply
449
views
Nothing happens when running GATK VCF Validate Variants. Output warning: processed 0 (zero) total variants
GATK
VCF
snp
ValidateVariants
updated 1 day ago by
Pierre Lindenbaum
165k • written 2 days ago by
maikejet
• 0
0
votes
1
reply
192
views
Annotate GWAS result gene function from GFF file
gwas
gff
gff3
annotation
updated 2 days ago by
lieven.sterck
15k • written 2 days ago by
alnus
• 0
0
votes
0
replies
129
views
WGCNA sample-data preprocessing order
gene-expression
wcgna
microarray
network
data-preprocessing
2 days ago by
Reuben
• 0
6
votes
3
replies
1.3k
views
drug sensitivity prediction
deseq2
oncopredict
R
drug
updated 3 days ago by
Luka
• 0 • written 2.2 years ago by
luffy
▴ 130
1
vote
1
reply
193
views
VCFfiltering
VCF
BCFtools
FreeBayes
updated 21 hours ago by
Mark
★ 1.6k • written 3 days ago by
Peter
• 0
0
votes
0
replies
174
views
Clumping- cannot mtfrm
clumping
MR
updated 3 days ago by
GenoMax
148k • written 3 days ago by
sp
• 0
0
votes
0
replies
196
views
Analysis and Verification of Mathematical Equations in the Theory of Consciousness
Consciousness
brian
Neuron
neurobiology
updated 3 days ago by
GenoMax
148k • written 3 days ago by
steklolampa
• 0
0
votes
0
replies
194
views
Genetic Trio Phasing with EAGLE2 using hg38
trios
haplotype
phasing
genetics
4 days ago by
heskett
▴ 110
5
votes
3
replies
341
views
b37 liftover
b37
liftover
3 days ago by
spesks
• 0
0
votes
0
replies
187
views
Plugging output files from phyluce phasing workflow into Structure
phyluce
uce
bam
phasing
structure
4 days ago by
gabe.somarriba
• 0
0
votes
0
replies
189
views
gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short:
header
pacbio
bam
basecaller
gcpp
4 days ago by
therosng
• 0
0
votes
1
reply
242
views
circos ignoring the ticks and plots
diagram
circos
updated 4 days ago by
GenoMax
148k • written 4 days ago by
baibhu1234
• 0
3
votes
4
replies
403
views
Strange offsetting in deeptools?
deeptools
3 days ago by
Elijah
▴ 10
0
votes
3
replies
292
views
Merging gvcf files between Dragen and other calling tools
gvcf
merge
bcftools
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
tacrolimus
▴ 140
7
votes
6
replies
464
views
Download SRA raw data using efetch
sra-toolkit
efetch
biopython
4 days ago by
biofysikos
• 0
0
votes
7
replies
398
views
Issue with CIBERSORTx Error 139
CIBERSORTX
docker
error193
updated 4 days ago by
jared.andrews07
★ 18k • written 4 days ago by
Hamdache
• 0
0
votes
0
replies
195
views
Repeat Modeler Database Generation
masker
modeler
genome
fungus
repeat
4 days ago by
SomeOne
▴ 160
0
votes
0
replies
187
views
How to scale data matrix in Seurat
Scale
4 days ago by
frarodmar17
• 0
0
votes
1
reply
241
views
Use Hi-C Sequence Data of close relative for scaffolding of genome.
assembly
genoem
fungus
HiC
sequencing
updated 4 days ago by
GenoMax
148k • written 4 days ago by
SomeOne
▴ 160
0
votes
1
reply
235
views
Box plot of gene expression data
boxplot
updated 4 days ago by
ATpoint
86k • written 4 days ago by
a.stef.44
▴ 10
120,143 results • Page
1 of 2403
Recent Votes
Creating pangenome graphs using vcf files?
Answer: STAR aligner - Is this still maintained?
Answer: Converting GP field in a VCF to GT
A: Extract subset of samples from multigenome vcf file
A: how to extract sample id with bcftools or vcftools
C: Extract uniquely mapped reads from bam file
Why some lines of BAM file do not contain NH tag
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Comment: chromHMM annotations
by
Bioinformatics_16
• 0
@i.sudbery Thank You
Answer: How to trim sequences
by
Mensur Dlakic
★ 28k
Generally speaking, your don't trim individual sequences. Rather, you align them first and then trim the alignment. I will give you links t…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam
by
samdegregori
• 0
@mensur apologies on subjecting you to such a trivial troubleshooting error. Hitting myself on the head because I was thinking fa and fna w…
Comment: How to download metadata for the Broad Firehose RNA-seq data?
by
GenoMax
148k
You may want to get the data directly from GDC Portal/analysis center for the TCGA data: https://portal.gdc.cancer.gov/analysis_page?app=Pr…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam
by
Mensur Dlakic
★ 28k
I don't mean to sound harsh, but this is pretty basic stuff that is easily resolved if you read through the CheckM2 manual and follow the d…
Comment: Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the sam
by
samdegregori
• 0
Yeah that's what I was thinking but triple checked and it seems to be right. And yes of course here is the output for reference: runnin…
Comment: Interpreting Varied Survival Times in TCGA-BRCA Data
by
mebius_band
• 0
Sorry for interrupting your question but can I ask you where you find the data on what samples belong to healthy patients and what sample t…
Answer: Interpreting Varied Survival Times in TCGA-BRCA Data
by
wenbinm
▴ 40
I don't see why "samples with a survival outcome of 1" can't "have longer survival times than those where the survival outcome is 0"? Sampl…
Comment: gene annotation tool recommendations for oomycetes
by
GenoMax
148k
Oomycetes have pretty complex genomes (most of it repeats as I recall from working with one in distant past) so it would help a lot if you …
Comment: How to compare gene prediction
by
Mensur Dlakic
★ 28k
I think the first part of your advice is on point. However, I don't see the logic with this part: > One possible solution is to align all …
Answer: Web- based bioinformatics tool/s for identification of cysteine-rich proteins
by
Mensur Dlakic
★ 28k
There is a subset of BioPython called [**SeqIO**](https://biopython.org/wiki/SeqIO) with many examples of how to read and manipulate biolog…
Comment: constructing de novo assembly of plant short reads
by
Dave Carlson
★ 2.1k
You can just concatenate the various R1 and R2 fastq files before running the assembly. Let's say you have two samples (sample1, sample2),…
Comment: Reducing runtime of low-score alignments
by
Mensur Dlakic
★ 28k
Python is not very efficient for that type of work. There are all kinds of existing tools that are much faster: BLAST, FASTA and DIAMOND ar…
Comment: constructing de novo assembly of plant short reads
by
analyst
▴ 50
Do you mean merging of fastq files and running assembly on merged fastq file? For example for MaSuRCA I found following command that seems…
Comment: constructing de novo assembly of plant short reads
by
Dave Carlson
★ 2.1k
If you have multiple samples from the same species, you can just combine the fastq files and generate a single assembly.
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