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121,938 results • Page
139 of 2439
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
2.0k
views
Error in changing the annotation color of pheatmap
R
package
pheatmap
updated 18 months ago by
fracarb8
★ 1.7k • written 18 months ago by
applepie
▴ 10
0
votes
0
replies
477
views
News:
Call for abstract: Quest for Orthologs meeting in Montreal
conference
phylogeny
comparativegenomics
orthology
evolution
18 months ago by
sina.majidian
▴ 20
0
votes
2
replies
778
views
How to interpret merged_calls result of command line from CNVpytor
CNVpytor
updated 18 months ago by
GenoMax
154k • written 18 months ago by
Nannapat
• 0
0
votes
1
reply
2.8k
views
Segmentation fault for cd-hit
software-error
updated 18 months ago by
GenoMax
154k • written 10.5 years ago by
Crystal
▴ 70
3
votes
2
replies
1.1k
views
How do I collapse rows of a tibble in R?
R
tidyverse
tibble
collapse
18 months ago by
BioinfGuru
★ 2.1k
0
votes
6
replies
1.9k
views
cutadapt tool
cutadapt
updated 18 months ago by
Brian Bushnell
20k • written 2.2 years ago by
Eshwari
▴ 10
0
votes
1
reply
910
views
Sequence Duplication Levels in targeted sequencing
fastqc
pcr
sequencing
updated 18 months ago by
Brian Bushnell
20k • written 19 months ago by
Shaghayegh
▴ 20
3
votes
6
replies
1.6k
views
Target deletions with adaptive sampling
microdeletions
nanopore
AdaptiveSampling
18 months ago by
njornet
▴ 20
1
vote
5
replies
6.8k
views
6 follow
how to know what adapter sequences to trim for RNA-seq?
fastq
RNA-seq
cutadapt
updated 18 months ago by
Brian Bushnell
20k • written 2.5 years ago by
lunarskye222
▴ 10
2
votes
3
replies
1.6k
views
Variant caller for Ion Torrent data
ThermoFisher
NGS
IonTorrent
Genomics
Variant-Calling
updated 18 months ago by
Brian Bushnell
20k • written 19 months ago by
adarsh
▴ 60
12
votes
12
replies
2.9k
views
Processing fastq files for genome assembly
fastq
vcf
assembly
amino-acid
updated 18 months ago by
Brian Bushnell
20k • written 19 months ago by
Neil
▴ 20
0
votes
0
replies
495
views
different protocols for rapid nanopore sequencing starting from solid tumor
solid
tumor
nanopore
oxford
sequencing
updated 18 months ago by
GenoMax
154k • written 18 months ago by
LauferVA
4.8k
0
votes
0
replies
437
views
Questions regarding Boundary Conditions for Adaptive Sequencing for Oxford Nanopore
adaptive
sampling
nanopore
oxford
sequencing
18 months ago by
LauferVA
4.8k
0
votes
2
replies
1.0k
views
Problem merging plink files for somatic variants.
plink
somatic
vcf
18 months ago by
Palgrave
▴ 140
4
votes
8
replies
1.4k
views
i'm trying to use STAR and there is a problem...
STAR
updated 18 months ago by
GenoMax
154k • written 18 months ago by
markusz
▴ 10
0
votes
2
replies
1.4k
views
Warning: Expected at least 2 parts in FORMAT entry: ID=GP,Number=3,Type=Float,Description="Estimated Posterior Probabilities for Genotypes 0/0, 0/1 a…
vcftools
updated 18 months ago by
Pierre Lindenbaum
166k • written 18 months ago by
juan.sainz
• 0
0
votes
0
replies
483
views
Gene Prediction Breaker3
prediction
protein-seq
GTF
Breaker3
gene
18 months ago by
mathavanbioinfo
▴ 80
4
votes
2
replies
1.2k
views
Forum:
Exploring Amino Acid Patterns in Proteins Through N-gram Analysis
protein
CAFA5
18 months ago by
Anatoly A.
▴ 10
0
votes
2
replies
790
views
How to save the output of VARSCAN results in different vcf names?
snv
slurm
output
varscan
18 months ago by
kabir.deb
▴ 90
1
vote
5
replies
1.2k
views
Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
sraexplorer
sratoolkit
updated 18 months ago by
GenoMax
154k • written 18 months ago by
biotrekker
▴ 110
9
votes
7
replies
1.9k
views
Getting fasta file from the VCF after variant calling
fastq
pangolin
assembly
updated 18 months ago by
Michael
56k • written 19 months ago by
Neil
▴ 20
1
vote
1
reply
721
views
convert and merge somatic vcf file to plink format
gwas
plink
vcf
updated 18 months ago by
LChart
5.1k • written 18 months ago by
Palgrave
▴ 140
3
votes
1
reply
696
views
Get read counts without GTF/GFF files
RNA-seq
updated 18 months ago by
GenoMax
154k • written 18 months ago by
weather
• 0
1
vote
0
replies
401
views
Using TidyEstimate scores in the Design Matrix of DESeq2
ESTIMATE
deseq2
TidyESTIMATE
RNAseq
18 months ago by
Abhishek
▴ 10
0
votes
6
replies
1.2k
views
why the file is low after combining the Hi-C reads using Arima genomics pipeline of mapping
bwa
mapping
genome
samtools
plants
18 months ago by
rj.rezwan
▴ 20
0
votes
0
replies
495
views
DESeq stats or Wilcoxon auc scores as input in pathway analysis
pathway-analysis
updated 18 months ago by
Ram
45k • written 19 months ago by
leranwangcs
▴ 150
0
votes
0
replies
409
views
Experience with copykat
copykat
19 months ago by
Nona
▴ 90
0
votes
1
reply
689
views
Analyzing scRNA seq data and want to analyze it's DEG with DESeq2
scRNA-seq
DEG
DESeq2
19 months ago by
kayah
▴ 20
3
votes
4
replies
918
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
19 months ago by
Aleksandr
▴ 10
3
votes
12
replies
2.6k
views
bbmap read length from fastq
fastq
bbmap
updated 18 months ago by
GenoMax
154k • written 19 months ago by
marco.barr
▴ 180
2
votes
1
reply
777
views
how to add non-reference genes to BED file of intervals for PHG
pangenome
plants
PHG
updated 19 months ago by
lcj34
▴ 420 • written 19 months ago by
b.contreras.moreira
▴ 490
4
votes
2
replies
767
views
GFF reformator
gff
updated 19 months ago by
GenoMax
154k • written 19 months ago by
HERMAN
▴ 10
0
votes
0
replies
460
views
featureCounts micounts reads?
RNA-seq
GTF
introns
featureCounts
19 months ago by
tessa2525
• 0
0
votes
1
reply
741
views
Having problems doing the Hisat2 alignment
hisat2
updated 19 months ago by
ATpoint
89k • written 19 months ago by
2385676601
• 0
2
votes
3
replies
1.3k
views
Inflation in Imputed data
genomic
immunochip
inflation
topmed
updated 19 months ago by
Amy
▴ 20 • written 3.4 years ago by
desicasares
▴ 40
0
votes
0
replies
377
views
Tools for eQTL and somatic mutation analysis of RNA-seq data
eqtl
somatic-mutations
rna-seq
updated 18 months ago by
Ram
45k • written 19 months ago by
malonzm1
▴ 20
5
votes
3
replies
1.7k
views
SHAPEIT5 phasing
SHAPEIT
VCF
SHAPEIT5
18 months ago by
Michal Frenkel
▴ 30
0
votes
1
reply
846
views
Running Pangolin
Pangolin
Splicing
updated 18 months ago by
Ram
45k • written 19 months ago by
Sruthi
• 0
2
votes
2
replies
1.0k
views
Re. Batch effect correction in data with a design matrix without full rank
deseq2
batch
multi-factor
updated 19 months ago by
swbarnes2
15k • written 19 months ago by
JB
• 0
0
votes
7
replies
1.8k
views
RNA Seq Sample Outlier
MDS
RNA-Seq
updated 19 months ago by
ATpoint
89k • written 19 months ago by
Emilie
▴ 10
0
votes
3
replies
2.8k
views
ANGeS - Ancestral Genome reconstruction
ancestral
genome
updated 19 months ago by
illodukarthickbabu
• 0 • written 4.1 years ago by
alslonik
▴ 320
0
votes
13
replies
2.6k
views
Help with the new nomenclature of multi-nucleotide variants
bam
igv
multinucleotide
18 months ago by
amy__
▴ 250
1
vote
5
replies
1.6k
views
index fasta file for HaplotypeCaller
Samtools
HaplotypeCaller
GATK
faidx
18 months ago by
Mojtaba
• 0
0
votes
7
replies
1.3k
views
single nuclei sequencing questions
fastq
single-nuclei-sequencing
updated 18 months ago by
Ram
45k • written 19 months ago by
Long
▴ 10
2
votes
1
reply
806
views
DESeq and SVA for batch effect
sva
limma
batch-effect
DESeq2
updated 19 months ago by
LChart
5.1k • written 19 months ago by
michelafrancesconi9
▴ 20
3
votes
4
replies
1.1k
views
How to merge VCF files from multiple samples and remove individual level information
VCF
19 months ago by
Arton
▴ 20
2
votes
3
replies
1.1k
views
How to download all expressed sequence tags (ESTs) for particular species from NCBI using command ?
NCBI
EST
updated 19 months ago by
GenoMax
154k • written 19 months ago by
Sony
▴ 20
0
votes
1
reply
717
views
How is it possible to differentiate CG or AT heterozygous in Illumina Infinium Genotype Microarrays?
Heterozygous
Genotype
Microarray
Infinium
Illumina
updated 19 months ago by
LChart
5.1k • written 19 months ago by
igor.alcaras
• 0
0
votes
0
replies
555
views
Adding shapes from plotly R library to the phylogenetic tree tips generated by ggtree
R
phylogenetic-tree
ggtree
plotly
updated 19 months ago by
Ram
45k • written 19 months ago by
Hann
▴ 130
2
votes
7
replies
1.6k
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
18 months ago by
b2003
• 0
121,938 results • Page
139 of 2439
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Comment: Linear regression vs DESeq2 models for DEG analysis
Answer: Linear regression vs DESeq2 models for DEG analysis
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Recent Replies
Comment: Feasibility of detecting PCR-chimeric reads with Machine Learing (ML) for organe
by
andres.firrincieli
3.9k
While there is no specific rule against the use of ChatGPT or similar, this must be clearly stated in the answer
Comment: cellranger mkref fail/error
by
Arup Ghosh
3.4k
As you managed to run each organism separately successfully. Does the combined size of the FASTA files exceed the amount of memory you spec…
Comment: different methods target identification
by
ATpoint
89k
Oh come on... https://www.biostars.org/p/75548/ https://www.biostars.org/p/357878/
Answer: Feasibility of detecting PCR-chimeric reads with Machine Learing (ML) for organe
by
teamardigen
• 0
Your idea is definitely feasible on Illumina reads. Since curated chimera datasets are rare, most people simulate them in silico (concatena…
Comment: Linear regression vs DESeq2 models for DEG analysis
by
ATpoint
89k
+1 Your answer should be the top-voted answer in this thread https://www.biostars.org/p/284775/ as it actually addresses conceptual diffe…
Comment: Linear regression vs DESeq2 models for DEG analysis
by
swbarnes2
15k
It is not clear to me that you can meaningfully correct for 5 different batches with two samples a piece.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
GenoMax
154k
> I am not sure if there would be primer dimer sequences I should have said adapter dimers above. Correction made.
Comment: Help understanding this per base sequence content failure fastqc plot
by
lieven.sterck
15k
that 151st base added is a base to ignore (it's a kind of random addition) ... if I recall correctly it's a consequence of the technology. …
Comment: Linear regression vs DESeq2 models for DEG analysis
by
FioG
• 0
@swbarnes2 Thank you for your response! I am new to RNA seq analysis and was originally recommended to use the LM method following cqn and …
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment?
by
curious
▴ 890
Thank you, the adapter sequences are specified as CTGTCTCTTATACACATCT+ATGTGTATAAGAGACA is the SampleSheet.csv file from the sequencing run.…
Comment: how to explain the sample size discrepancy in UCSC Xena
by
nuorain
▴ 40
Thank you very much.
Answer: how to explain the sample size discrepancy in UCSC Xena
by
i.sudbery
22k
Because there wasn't RNA-seq analysis performed for every sample in TCGA?
Answer: Linear regression vs DESeq2 models for DEG analysis
by
i.sudbery
22k
There are two main problems with using linear models for read-count based analyses. Firstly, linear models assume a normal distribution…
Comment: real time PCR data analysis
by
ATpoint
89k
I cannot guide on GraphPad. It's commercial software so better contact their support.
Answer: Linear regression vs DESeq2 models for DEG analysis
by
swbarnes2
15k
DE genes in bulk RNASeq is what DESeq2 was made for, so why wouldn't you use it? RPKM is not an appropriate normalization method here. M…
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