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547 results • Page
1 of 11
Sort: replies
Rank
Views
Votes
Replies
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 14 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 7 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
21 days ago by
b.contreras.moreira
▴ 170
4
votes
13
replies
841
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 7 days ago by
BioinfGuru
★ 1.7k • written 12 days ago by
matteo.levorato
• 0
2
votes
12
replies
720
views
Nanopore data filtering using fastp
fastp
nanopore
26 days ago by
emilydolivo97
▴ 10
3
votes
12
replies
486
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
21 days ago by
Lila M
★ 1.2k
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 28 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
0
votes
10
replies
296
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
3 hours ago by
atowns21
• 0
2
votes
10
replies
814
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 26 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 6 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
8
votes
10
replies
688
views
bash script
whole-genome-sequencing
updated 8 days ago by
Ram
43k • written 15 days ago by
bestone
▴ 30
0
votes
10
replies
606
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
22 days ago by
dzisis1986
▴ 70
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 7 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
9
replies
737
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 5 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
9
replies
571
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 12 days ago by
LauferVA
4.2k • written 13 days ago by
Aki
▴ 10
0
votes
9
replies
474
views
Low number of both surviving reads after trimming
trimmomatic
trimming
26 days ago by
Jay
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 7 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
4
votes
9
replies
561
views
variant calling
variant-calling
updated 20 days ago by
Ram
43k • written 21 days ago by
dalibenam64
• 0
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 14 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
0
votes
8
replies
515
views
STAR aligner options
STAR
26 days ago by
theophile
• 0
0
votes
8
replies
259
views
Error in cnetplot enrichplot package
R
updated 1 day ago by
Ram
43k • written 1 day ago by
Farhad
• 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 14 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 6 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 7 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
0
votes
7
replies
409
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 27 days ago by
GenoMax
141k • written 27 days ago by
Patadu94
• 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 15 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
7
replies
554
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 22 days ago by
cmdcolin
★ 3.8k • written 25 days ago by
I0110
▴ 140
2
votes
7
replies
799
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 6 days ago by
quentinperriere
• 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 14 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
1
vote
7
replies
882
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 28 days ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
4
votes
7
replies
535
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 10 days ago by
Ram
43k • written 11 days ago by
AHerik
▴ 20
0
votes
7
replies
395
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 18 days ago by
Papyrus
★ 2.9k • written 19 days ago by
doramora
▴ 10
2
votes
6
replies
625
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 21 days ago by
Ram
43k • written 4 months ago by
zea
• 0
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 14 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
5
votes
6
replies
387
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 21 days ago by
Istvan Albert
100k • written 22 days ago by
Pumla
• 0
0
votes
6
replies
536
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
8 days ago by
Dunois
★ 2.5k
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 7 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
2
votes
6
replies
855
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 7 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
4
votes
6
replies
830
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 21 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
0
votes
6
replies
450
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
14 days ago by
marongiu.luigi
▴ 710
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2
RNA-Seq
Differential-gene-Expression
updated 14 days ago by
Ram
43k • written 5.7 years ago by
Pin.Bioinf
▴ 340
2
votes
6
replies
393
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
15 days ago by
jkim
▴ 170
0
votes
6
replies
610
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 14 days ago by
Ram
43k • written 4 months ago by
tw_140
• 0
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 8 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
2
votes
6
replies
524
views
Need help understanding core SNPs
SNPs
snippy
29 days ago by
ujichu
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 3 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
0
votes
5
replies
483
views
How to assure that sequence consensus is genuine?
genome
17 days ago by
marongiu.luigi
▴ 710
0
votes
5
replies
370
views
Parsing fasta file by coordinates
linux
fasta
updated 26 days ago by
GenoMax
141k • written 29 days ago by
sorrymouse
▴ 120
3
votes
5
replies
405
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
updated 20 days ago by
GenoMax
141k • written 21 days ago by
e.r.zakiev
▴ 200
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 7 days ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
547 results • Page
1 of 11
Recent Votes
Comment: Per base sequence content error in RNAseq analysis
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Gene set enrichment analysis differences between 2020 and 2024
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
Comment: TCGA2STAT Error: Firehose connection
Answer: HaplotypeCaller - only SNPs
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Comment: How to compare the quality of assemblies
by
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▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
by
Istvan Albert
100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs
by
analyst
▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Answer: Wilcox test using data slot (log normalized count values) of scRNA-seq between t
by
yxwucq
• 0
The best way is to generate a pseudo-bulk aggregation then apply edgeR or DESeq2. You can also directly use wilcoxon on sc-level, since man…
Comment: How to solve this RoseTTAFold colaboratory error?
by
Mensur Dlakic
★ 27k
There is a dedicated Discord group that deals with everything related to ColabFold and its derivatives. Below is an invitation to join that…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie
by
atowns21
• 0
Hmm, okay I'm not sure what is going on, but here is what I did: 1. Downloaded a single fastq: `parallel-fastq-dump --tmpdir . --threads …
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Ok, thank you so much~
Comment: GTF file for Rhinolophus sinicus
by
GenoMax
141k
I was able to get the GTF file. I tried the fasta genome and it seemed to work but I did not complete the download. If you choose to ignore…
Comment: some error in building kraken2 database
by
Art1ess
• 0
I have 2 files output, no error logs... the .kreport file: 100.00 160136511 160136511 U 0 unclassified head .res…
Comment: TCGA2STAT Error: Firehose connection
by
LauferVA
4.2k
agree. from a data-centric (rather than software centric) standpoint, it shouldn't be hard to get the TCGA data you are looking for from o…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
yep. in this case id definitely start with the grant numbers themselves as others have indicated. i did not recommend this before due to un…
Comment: GTF file for Rhinolophus sinicus
by
atowns21
• 0
This download doesn't seem to work for me. There is a message on the website saying "Warning: contaminated. Status: RefSeq GCF_001888835.1 …
Answer: HaplotypeCaller - only SNPs
by
Pierre Lindenbaum
161k
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
Answer: Gene set enrichment analysis differences between 2020 and 2024
by
geneontologyhelp
▴ 380
We have releases about monthly in order to keep our data accurate and reflect current understanding. In 4 years, there have been about 40 r…
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