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368 results • Page
3 of 8
Sort: replies
Rank
Views
Votes
Replies
2
votes
4
replies
274
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by
kirill.zaslavsky
• 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 22 hours ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
0
votes
4
replies
320
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
4 days ago by
pablo
▴ 300
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 22 hours ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation
RNA-Seq
R
updated 2 days ago by
Ram
43k • written 6.0 years ago by
mannoulag1
▴ 120
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 22 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 22 hours ago by
Ram
43k • written 18 months ago by
Dominique
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 22 hours ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
1
vote
4
replies
601
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 1 day ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
3
votes
4
replies
362
views
biomaRt error for different R version
biomaRt
R
updated 1 day ago by
GenoMax
141k • written 2 days ago by
manaswwm
▴ 490
0
votes
4
replies
432
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
1 day ago by
feather-W
• 0
2
votes
4
replies
333
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 4 days ago by
GenoMax
141k • written 4 days ago by
Sony
▴ 10
3
votes
4
replies
398
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
updated 1 day ago by
GenoMax
141k • written 1 day ago by
n_navy
• 0
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 4.6 years ago by
Victoria
▴ 10
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 2 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
5
votes
4
replies
255
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
3 days ago by
Spring
• 0
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 2 days ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
0
votes
4
replies
484
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
10 hours ago by
Kai Xin
• 0
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 5.9 years ago by
Poorya Parvizi
▴ 60
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 1 day ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 1 day ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
3
votes
4
replies
351
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
Sony
▴ 10
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 1 day ago by
Ram
43k • written 4.6 years ago by
dmj6ab
▴ 20
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 2 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 2 days ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma
microarray
bioconductor
R
updated 2 days ago by
Ram
43k • written 6.3 years ago by
Raheleh
▴ 260
1
vote
3
replies
399
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 3 days ago by
LChart
3.9k • written 4 days ago by
leranwangcs
▴ 120
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor
limma
sva
r
batch-effect
updated 22 hours ago by
Ram
43k • written 7.6 years ago by
Lluís R.
★ 1.2k
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt
R
updated 2 days ago by
Ram
43k • written 3.8 years ago by
mbk0asis
▴ 680
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 22 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 3 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
2
votes
3
replies
965
views
Treating "patient" as a batch effect
ComBat_seq
DESeq2
batch-Effect
updated 2 days ago by
Ram
43k • written 17 months ago by
Mia
▴ 20
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression
transcriptome
updated 22 hours ago by
Ram
43k • written 8.9 years ago by
siddharth.patel.153
• 0
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 3 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat
R
SVA
Biostatistics
batch-effect
updated 22 hours ago by
Ram
43k • written 7.4 years ago by
mkhadka10
• 0
1
vote
3
replies
392
views
Extracting data from a local NCBI taxonomy database
R
NCBI
xml
E-utilities
Blast
updated 5 days ago by
josev.die
▴ 60 • written 18 days ago by
Begonia_pavonina
▴ 150
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 22 hours ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony
single-cell
scRNA-seq
batch-effect
updated 22 hours ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
2
votes
3
replies
345
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 4 days ago by
ATpoint
81k • written 5 days ago by
IM
• 0
1
vote
3
replies
818
views
add INFO tag to vcf with bcftools
bcftools
vcf
updated 3 days ago by
Ram
43k • written 23 months ago by
from the mountains
▴ 230
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 22 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
2
votes
3
replies
243
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 3 days ago by
GenoMax
141k • written 3 days ago by
lorena9132
• 0
0
votes
3
replies
299
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 6 days ago by
ATpoint
81k • written 8 days ago by
gdfsnkfns
• 0
2
votes
3
replies
253
views
Editing Human Reference Genome by adding a CDS
gff
agat
transcriptome
updated 2 days ago by
Michael
54k • written 2 days ago by
LDT
▴ 330
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 22 hours ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 22 hours ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
1
vote
3
replies
313
views
Ensembl gene id conversion
biomart
ensembl
updated 3 days ago by
ATpoint
81k • written 5 days ago by
naveedhasan2000
• 0
1
vote
3
replies
389
views
Limma compare between 3 conditions vs 2 conditions
Limma
updated 2 days ago by
Gordon Smyth
★ 7.0k • written 24 days ago by
Chris
▴ 260
2
votes
3
replies
370
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
1 day ago by
valentinatsar
• 0
3
votes
3
replies
377
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
2 days ago by
ayushm64
• 0
368 results • Page
3 of 8
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Answer: Cellranger count error: Input FASTQ file ended prematurely
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Dear all, The reason for the error was due to the index (I1) fastq files, for example `SI-GA-A1_1_S1_L001_I1_001.fastq.gz` having a lo…
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Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues
by
_quantum_girl_
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They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis
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★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis
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The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
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Enrique
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Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
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The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
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Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
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81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
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Carlo Yague
8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
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For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors.
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Dinmukhamed
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I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file
by
Maria
• 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
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