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900 results • Page
6 of 18
Sort: replies
Rank
Views
Votes
Replies
2
votes
4
replies
6.1k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 26 days ago by
Ram
43k • written 7.7 years ago by
gokce.ouz
▴ 70
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 1 day ago by
Fungal genetics
• 0 • written 7.1 years ago by
ntyagi654
• 0
1
vote
4
replies
381
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
7 days ago by
heelpPlease
• 0
0
votes
4
replies
654
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
26 days ago by
Kai Xin
• 0
2
votes
4
replies
385
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 21 days ago by
swbarnes2
14k • written 22 days ago by
dxj294
• 0
1
vote
4
replies
383
views
Segmentation error while using a tool
smalt
updated 10 days ago by
Mensur Dlakic
★ 27k • written 11 days ago by
Ruqaiya
• 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 27 days ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq
batch-effect
R
updated 27 days ago by
Ram
43k • written 4.8 years ago by
jperezboza
▴ 20
0
votes
4
replies
290
views
Genbank File Format
gbkformat
14 days ago by
alenew.am
• 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 27 days ago by
Ram
43k • written 5.2 years ago by
grant.hovhannisyan
★ 2.6k
0
votes
4
replies
611
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 24 days ago by
ATpoint
82k • written 25 days ago by
rheab1230
▴ 140
3
votes
4
replies
443
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 8 days ago by
Gordon Smyth
★ 7.2k • written 11 days ago by
SHN
▴ 40
5
votes
4
replies
378
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
28 days ago by
Spring
• 0
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 20 days ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
3
votes
4
replies
527
views
biomaRt error for different R version
biomaRt
R
updated 26 days ago by
GenoMax
142k • written 27 days ago by
manaswwm
▴ 510
1
vote
4
replies
479
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 21 days ago by
atowns21
• 0 • written 6 months ago by
ara
• 0
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 26 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
4
replies
321
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 15 days ago by
Ram
43k • written 15 days ago by
Hamtaro
▴ 50
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 6 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.5k
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 26 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
6
votes
4
replies
425
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
12 days ago by
Estevão
▴ 10
5
votes
4
replies
2.9k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 28 days ago by
hamarillo
▴ 70 • written 5.7 years ago by
silviajserrano
▴ 50
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 4.7 years ago by
Victoria
▴ 10
2
votes
4
replies
403
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
21 days ago by
HyperEvo
• 0
1
vote
4
replies
293
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 hours ago by
Juke34
8.6k • written 1 day ago by
Vijith
▴ 30
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq
Differential-Expression
batch-effect
updated 26 days ago by
Ram
43k • written 5.1 years ago by
georgians
▴ 50
0
votes
4
replies
227
views
Galaxy StringTie error
stringtie
galaxy
20 hours ago by
trkfs
• 0
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 25 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
256
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 1 day ago by
Ram
43k • written 14 days ago by
Adyasha
• 0
1
vote
3
replies
443
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 16 days ago by
Mensur Dlakic
★ 27k • written 18 days ago by
O.rka
▴ 720
1
vote
3
replies
369
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 16 days ago by
ATpoint
82k • written 17 days ago by
Francesco
▴ 10
2
votes
3
replies
257
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
1 day ago by
Azra
▴ 10
1
vote
3
replies
146
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 9 hours ago by
Ram
43k • written 10 hours ago by
Prawesh
• 0
1
vote
3
replies
251
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 5 days ago by
GenoMax
142k • written 6 days ago by
cput
• 0
0
votes
3
replies
171
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 1 day ago by
Ram
43k • written 1 day ago by
yau
• 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 26 days ago by
Ram
43k • written 7.7 years ago by
Lluís R.
★ 1.2k
6
votes
3
replies
225
views
Interpretting IGV output
IGV
updated 22 days ago by
Carlo Yague
8.7k • written 23 days ago by
analyst
▴ 50
1
vote
3
replies
358
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 27 days ago by
Pierre Lindenbaum
161k • written 4 weeks ago by
giulia.cosenza
• 0
0
votes
3
replies
554
views
JASPAR2024_getMatrixSet error
JASPAR2024
getMatrixSet
updated 5 days ago by
Ram
43k • written 12 weeks ago by
maplewj
▴ 10
1
vote
3
replies
343
views
DESeq2 processing problems
deseq2
R
updated 13 days ago by
ATpoint
82k • written 13 days ago by
jagdish7921
• 0
4
votes
3
replies
429
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 17 days ago by
Arup Ghosh
3.2k • written 18 days ago by
chaco001
▴ 40
0
votes
3
replies
434
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 21 days ago by
colindaven
6.4k • written 29 days ago by
rj.rezwan
• 0
0
votes
3
replies
458
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
14 days ago by
Assa Yeroslaviz
★ 1.8k
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 26 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
1
vote
3
replies
303
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 11 days ago by
ATpoint
82k • written 12 days ago by
Qi
• 0
3
votes
3
replies
329
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 1 day ago by
Mathew
▴ 140 • written 4 days ago by
Christopher
• 0
1
vote
3
replies
886
views
add INFO tag to vcf with bcftools
bcftools
vcf
updated 28 days ago by
Ram
43k • written 2.0 years ago by
from the mountains
▴ 230
1
vote
3
replies
271
views
Odd alignment question/finding
Alignment
updated 11 days ago by
barslmn
★ 2.1k • written 13 days ago by
poordumbsillyidiot
• 0
3
votes
3
replies
365
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 19 days ago by
swbarnes2
14k • written 19 days ago by
M
• 0
0
votes
3
replies
241
views
Software to separate reads from different individuals
software
development
nanopore
updated 15 days ago by
GenoMax
142k • written 15 days ago by
njornet
▴ 20
900 results • Page
6 of 18
Recent Votes
Comment: Bamutils/ClipOverlap
Comment: How to calculate coverage of Nanopore long read data?
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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jen
▴ 10
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Recent Replies
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment
by
a.alnawfal.1992
▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data?
by
Arton
• 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
mbrav005
• 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon
by
sansan_96
▴ 90
..........
Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
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