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Limit : this week
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248 results • Page
2 of 5
Sort: Votes
Rank
Views
Votes
Replies
3
votes
4
replies
640
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
2 days ago by
rahu
• 0
3
votes
3
replies
177
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Estevão
• 0
2
votes
2
replies
392
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
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 6 days ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
2
votes
1
reply
256
views
Pediococcus acidilactici sequence analysis
BLAST
Gene-Ontology
updated 6 days ago by
Ram
43k • written 6 days ago by
anasjamshed
▴ 120
2
votes
6
replies
5.2k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 6 days ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
2
votes
7
replies
803
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
2
votes
3
replies
180
views
from row count to tpm
tpm
row-count
normalization
1 day ago by
michelafrancesconi9
▴ 20
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 6 days ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
2
votes
10
replies
720
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 6 days ago by
GenoMax
141k • written 7 days ago by
me
• 0
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 6 days ago by
Ram
43k • written 3.8 years ago by
i.sudbery
19k
2
votes
2
replies
369
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
6 days ago by
nhaus
▴ 300
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 6 days ago by
Ram
43k • written 18 months ago by
Dominique
• 0
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression
R
limma
batch-effect
model-matrix
updated 6 days ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 5 days ago by
ATpoint
82k • written 7.1 years ago by
boymin2020
▴ 80
2
votes
3
replies
936
views
Method to detect genome doubling
CNV
genome doubling
updated 2 days ago by
LauferVA
4.2k • written 4.5 years ago by
CY
▴ 750
2
votes
5
replies
422
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 3 days ago by
Lipika
• 0
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
12 hours ago by
samuelkalandarov2002
▴ 10
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 3 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 days ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
2
votes
5
replies
505
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 3 days ago by
Mensur Dlakic
★ 27k • written 4 days ago by
Giorgio
• 0
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 6 days ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
2
votes
4
replies
6.0k
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 6 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
2
votes
9
replies
777
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 19 hours ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
2
votes
4
replies
262
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
18 hours ago by
HyperEvo
• 0
2
votes
3
replies
405
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
6 days ago by
valentinatsar
• 0
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.6 years ago by
fractal61
▴ 10
2
votes
2
replies
143
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 16 hours ago by
analyst
▴ 30 • written 21 hours ago by
lorena9132
• 0
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
2
votes
1
reply
281
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 4 days ago by
GenoMax
141k • written 4 days ago by
rebecca.calvo
• 0
2
votes
5
replies
673
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
2
votes
1
reply
161
views
Seurat merge and batch correction
Seurat
updated 23 hours ago by
Ram
43k • written 1 day ago by
sooni
▴ 20
2
votes
3
replies
303
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.8k • written 15 days ago by
javanokendo
▴ 60
1
vote
1
reply
150
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
1
vote
1
reply
365
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
6 days ago by
otieno43
▴ 30
1
vote
4
replies
675
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 6 days ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat
microarray
meta-analysis
batch-effect
updated 6 days ago by
Ram
43k • written 9.9 years ago by
BrunoGiotti
▴ 120
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 6 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
1
vote
0
replies
2.1k
views
Tool:
DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq
scRNA-Seq
R
Batch-Effect
updated 6 days ago by
Ram
43k • written 6.9 years ago by
Ar
★ 1.1k
1
vote
1
reply
145
views
WGCNA preservation analysis
WGCNA
preservation
updated 1 day ago by
Michael
54k • written 1 day ago by
michael.flower.14
▴ 180
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 6 days ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
1
vote
5
replies
686
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 5 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
rrehimi
• 0
1
vote
0
replies
171
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
6 days ago by
Novogene
▴ 420
1
vote
5
replies
236
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 1 day ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
3
replies
187
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
1
vote
5
replies
288
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
1 day ago by
anasjamshed
▴ 120
1
vote
1
reply
409
views
Plink merge errors.
cygwin64
bed
PLINK
5 days ago by
Dinmukhamed
• 0
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 6 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray
Gene-expression
batch-effect
updated 6 days ago by
Ram
43k • written 6.9 years ago by
Shamim Sarhadi
▴ 220
248 results • Page
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Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
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Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
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You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
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I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
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We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
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14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
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14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
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