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121,939 results • Page
140 of 2439
Sort: Rank
Rank
Views
Votes
Replies
2
votes
7
replies
1.6k
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
18 months ago by
b2003
• 0
1
vote
1
reply
986
views
Filtering VCF files with bcftools
VCF
vcftools
bcftools
updated 19 months ago by
4galaxy77
2.9k • written 19 months ago by
eleni.psar
• 0
5
votes
2
replies
3.0k
views
Tool:
Coovar: Co-Occurring Variant Analyzer
snp
variant-annotation
updated 19 months ago by
GenoMax
154k • written 12.9 years ago by
Christian
★ 3.1k
0
votes
0
replies
379
views
Error in MetaPro pipeline at contig assembly
Metatranscriptomics
updated 19 months ago by
Ram
45k • written 19 months ago by
styagi
• 0
2
votes
5
replies
1.5k
views
Weird Fragment Length distribution multiQC
Salmon
RNA-seq
paired-end
MultiQC
updated 18 months ago by
GenoMax
154k • written 19 months ago by
_deb
• 0
2
votes
6
replies
1.3k
views
single cell RNA seq integration(Error in UseMethod(generic = "as.sparse", object = x))
scRNA-seq
19 months ago by
kayah
▴ 20
4
votes
2
replies
1.4k
views
no permission to install to directory
R
updated 19 months ago by
Ram
45k • written 19 months ago by
sooni
▴ 20
0
votes
5
replies
1.1k
views
Issues with bcftools
Bcftools
updated 19 months ago by
Pierre Lindenbaum
166k • written 19 months ago by
hgrsce
• 0
0
votes
5
replies
1.4k
views
Issues filtering VCF file with bcftools/vcftools
vcftools
vcf
bcftools
updated 18 months ago by
Pierre Lindenbaum
166k • written 19 months ago by
ekirsch
• 0
1
vote
9
replies
2.7k
views
blast retrieves "N/A" for taxonomic data
blast
blastn
updated 18 months ago by
flavianegrete
• 0 • written 4.8 years ago by
langziv
▴ 70
3
votes
4
replies
1.4k
views
Why many organisms even though they possess mitochondrial DNA (mtDNA), it is not typically represented by chromosomes labeled as "mtDNA"?
genome
mtDNA
reference-genome
sequence
19 months ago by
George X.
• 0
1
vote
6
replies
1.2k
views
RNA indexing using STAR error
RNA-seq
STAR
updated 19 months ago by
Ram
45k • written 19 months ago by
Shay
• 0
1
vote
2
replies
798
views
How to extract mutations in a particular gene from the VCF file of whole genome
NGS
mutations
VCF
19 months ago by
saamar.rajput
▴ 80
0
votes
3
replies
1.1k
views
Tools and software to visualize the moving cell compartments in 3D
3D-visualization
cell-compartments
19 months ago by
saamar.rajput
▴ 80
0
votes
0
replies
388
views
Computational tools for mapping potential epitope regions using mimotope-based methods
mimotope
phage
epitope
19 months ago by
ceciliadlcgg
• 0
0
votes
0
replies
410
views
Problem with blastdbcmd. “Error: [blastdbcmd] Skipped TRANSCRIPT/4865”
blast
updated 19 months ago by
Ram
45k • written 19 months ago by
elisamaarredondobel
• 0
0
votes
0
replies
810
views
Job:
Data scientist/Bioinformatician University of Wisconsin Biotechnology Center Bioinformatics Resource Center
data-scientist
updated 18 months ago by
Ram
45k • written 19 months ago by
jv
★ 1.9k
2
votes
3
replies
1.4k
views
STAR alignment setting for RNA-Seq data from mouse background expressing a human ortholog
alignment
star
ortholog
rna-seq
updated 19 months ago by
swbarnes2
15k • written 19 months ago by
marionette.kent
• 0
3
votes
5
replies
2.4k
views
(STAR) What causes a high number of reads that are unmapped because they are too short?
STAR
rna-seq
updated 19 months ago by
GenoMax
154k • written 19 months ago by
becky.reese
• 0
1
vote
1
reply
898
views
robust linear regression with interaction term
R
epigenetic
biostatistics
statistics
updated 19 months ago by
Jeremy
▴ 930 • written 19 months ago by
Bioinfonext
▴ 480
0
votes
3
replies
798
views
Help with mauve
mauve
updated 18 months ago by
Ram
45k • written 19 months ago by
reachedahead225
• 0
5
votes
5
replies
906
views
p-value on excel for different number of mutant samples vs WT samples
RNA-seq
biostatistics
updated 19 months ago by
ATpoint
89k • written 19 months ago by
abhatnagar
• 0
5
votes
6
replies
1.8k
views
Uploading HiC track on UCSC browser
custom_track
UCSC
HiC
updated 13 months ago by
Maximilian Haeussler
★ 1.8k • written 19 months ago by
arsala521
▴ 60
0
votes
5
replies
1.6k
views
Does salmon work with combined short and long read bam file?
salmon
updated 14 months ago by
callumjcparr
▴ 100 • written 20 months ago by
shinyjj
▴ 60
0
votes
1
reply
638
views
How does one create a custom VCF file?
genomics
VCF
updated 19 months ago by
Ram
45k • written 19 months ago by
manfi
▴ 20
0
votes
0
replies
485
views
Slow Python Script Pulling Metrics from Remora Oxford Nanopore
Nanopore
Remora
Long-Read
ONT
updated 19 months ago by
Ram
45k • written 19 months ago by
turcoa1
• 0
1
vote
2
replies
900
views
Considerations for nanopore adaptive sampling enrichment designing
adaptive-sampling
nanopore
19 months ago by
njornet
▴ 20
3
votes
3
replies
1.4k
views
Need help in using cutadapt to trim paired end fastq reads
fastq
primer
paried-end
cutadapt
updated 14 months ago by
Ram
45k • written 19 months ago by
George
• 0
2
votes
2
replies
770
views
WGCNA for co-expression network analysis
WGCNA
19 months ago by
Priya
• 0
0
votes
1
reply
507
views
Troubleshooting poor DP values
Illumina
GATK
updated 19 months ago by
Pierre Lindenbaum
166k • written 19 months ago by
manfi
▴ 20
2
votes
2
replies
876
views
Kmers unique mapping
KMC
alignment
bowtie
kmers
18 months ago by
enee
▴ 20
0
votes
0
replies
372
views
How to get the minimun branch distance tree?
distance
tree
phylogenetics
19 months ago by
Destineador
• 0
0
votes
0
replies
472
views
How can we deal with converted probe id in microarray?
R
microarray
probe
ensembl
updated 19 months ago by
Ram
45k • written 19 months ago by
wyt1995
▴ 40
0
votes
12
replies
2.2k
views
BWA MEM different synthax on linux (bash) and macOS (zsh)
MEM
BWA
19 months ago by
gernophil
▴ 130
4
votes
9
replies
2.4k
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
updated 19 months ago by
ATpoint
89k • written 2.3 years ago by
DanielEB_fisk
▴ 20
0
votes
0
replies
375
views
Issue opening modified .gff file in Artemis
gff
Artemis
updated 19 months ago by
Ram
45k • written 19 months ago by
A_heath
▴ 170
0
votes
0
replies
340
views
How can one determine if a sample size is representative in scRNA-seq analysis?
scRNA-seq
19 months ago by
fifty_fifty
▴ 90
47
votes
14
replies
22k
views
14 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 3 months ago by
BioNoobie
▴ 20 • written 5.0 years ago by
Hamid Ghaedi
3.3k
0
votes
1
reply
1.1k
views
Calculating Species Abundance/Richness in Excel
species-abundance
Excel
updated 19 months ago by
Ram
45k • written 19 months ago by
ilsa
• 0
2
votes
1
reply
651
views
RNAseq counts: transcript to gene
rnaseq
updated 19 months ago by
Ram
45k • written 19 months ago by
MAPK2
▴ 50
0
votes
2
replies
723
views
How can I have the structure of a gene (or haplotypes of a gene) on the top of the LD plot on Haploview
LDplot
Haploview
HaplotypeBlocks
LinkageFormat
19 months ago by
mona.patoughi
• 0
3
votes
7
replies
1.6k
views
Snakemake rule that runs an assessment for once after completing other previous rules
snakemake
19 months ago by
Fadlilah
▴ 10
0
votes
0
replies
590
views
Job:
Postdoctoral research position at the Barts Cancer Institute - Queen Mary University London
cancer
epigenomics
transposable-elements
updated 19 months ago by
Ram
45k • written 19 months ago by
Sergio Martínez Cuesta
▴ 230
0
votes
4
replies
1.1k
views
Can I perform a Functional Enrichment Analysis on a specific list of pre-defined genes?
RNA-seq
DGE
18 months ago by
Adam
• 0
0
votes
11
replies
2.4k
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 18 months ago by
barslmn
★ 2.4k • written 19 months ago by
avelarbio46
▴ 30
0
votes
7
replies
1.4k
views
PCR-cDNA sequence from MinION not alligned
minimap2
alignment
cDNA
19 months ago by
marco.barr
▴ 180
2
votes
7
replies
1.7k
views
Does vg call allow fuzzy match during SV calling?
vg
updated 19 months ago by
Jordan M Eizenga
▴ 760 • written 19 months ago by
Maxine
▴ 50
0
votes
1
reply
573
views
Mutation, MAF, CPTAC-3
CPTAC
mutation
updated 19 months ago by
marco.barr
▴ 180 • written 19 months ago by
Rob
▴ 180
5
votes
3
replies
1.2k
views
Single cell RNA sequencing analysis using R
scRNA-seq
updated 19 months ago by
Ram
45k • written 19 months ago by
fe.schiavetti
• 0
0
votes
6
replies
1.2k
views
Contamination in my FASTQC files
Fastqc
bowtie2
19 months ago by
carlosgonzalezcruz327
▴ 20
121,939 results • Page
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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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