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1,101 results • Page
2 of 23
Sort: replies
Rank
Views
Votes
Replies
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 26 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 1.9k
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 15 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 17 days ago by
Aspire
▴ 330 • written 18 months ago by
Manav
• 0
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 22 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
8
votes
10
replies
742
views
bash script
whole-genome-sequencing
updated 16 days ago by
Ram
43k • written 23 days ago by
bestone
▴ 30
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 26 days ago by
Ram
43k • written 6.5 years ago by
J.F.Jiang
▴ 920
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 15 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
1
vote
10
replies
971
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
7 days ago by
DKA
▴ 40
0
votes
10
replies
477
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 9 days ago by
Patadu94
• 0
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma
microarray
differential-gene-expression
updated 22 days ago by
Ram
43k • written 6.1 years ago by
fernardo
▴ 170
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 13 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 15 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
3
votes
10
replies
649
views
Piping samtools to R
R
NGS
bash
samtools
15 days ago by
noodle
▴ 580
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 14 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 2 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 16 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 18 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
4
votes
9
replies
590
views
variant calling
variant-calling
updated 28 days ago by
Ram
43k • written 29 days ago by
dalibenam64
• 0
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 15 days ago by
Ram
43k • written 5.8 years ago by
fp89
▴ 30
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 15 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
11
votes
9
replies
7.0k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 14 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 13 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
2
votes
9
replies
861
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 8 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 3 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
1
vote
9
replies
552
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
26 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
9
replies
564
views
frequency of each variant per sample
freebayes
variant-frequency
updated 27 days ago by
Pierre Lindenbaum
161k • written 28 days ago by
emilydolivo97
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
2 days ago by
anna
▴ 20
3
votes
9
replies
493
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 7 days ago by
Istvan Albert
100k • written 9 days ago by
Κοσμάς
• 0
0
votes
9
replies
612
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 20 days ago by
LauferVA
4.2k • written 21 days ago by
Aki
▴ 20
3
votes
9
replies
873
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 13 days ago by
Elisabeth Gasteiger
★ 2.4k • written 14 days ago by
Jacky
• 0
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 13 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 12 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
7
votes
8
replies
678
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 19 days ago by
spen
▴ 40 • written 22 days ago by
MBarcelo
▴ 40
1
vote
8
replies
702
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 22 days ago by
Anand Rao
▴ 630 • written 8 weeks ago by
bvm
▴ 20
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 14 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
1
vote
8
replies
431
views
Downsampling fastq file
downsample
fastq
1 day ago by
marco.barr
▴ 80
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 13 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
0
votes
8
replies
567
views
FreeBayes encountered a sudden error
freebayes
updated 27 days ago by
Michael
54k • written 27 days ago by
emilydolivo97
▴ 10
4
votes
8
replies
629
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 5 days ago by
Alex Reynolds
35k • written 6 days ago by
J
▴ 10
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 22 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
8
replies
407
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 1 day ago by
LauferVA
4.2k • written 3 days ago by
jinyu
▴ 10
0
votes
8
replies
361
views
Error in cnetplot enrichplot package
R
updated 9 days ago by
Ram
43k • written 9 days ago by
Farhad
• 0
1
vote
8
replies
848
views
Adding CB tag to bam file
samtools
bam
updated 7 days ago by
Pierre Lindenbaum
161k • written 13 days ago by
Maria
• 0
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 23 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 22 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
8
votes
8
replies
621
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 7 days ago by
swbarnes2
14k • written 8 days ago by
Aaliya
▴ 10
6
votes
8
replies
589
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 14 days ago by
dariober
14k • written 17 days ago by
manaswiniparija3
▴ 40
17
votes
8
replies
13k
views
9 follow
MAF vs VAF
sequencing
updated 29 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
7
votes
8
replies
687
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
27 days ago by
Riq
▴ 50
1,101 results • Page
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Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
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Comment: Odd alignment question/finding
by
ATpoint
82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets
by
ATpoint
82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding
by
liorglic
★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
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If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
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by
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• 0
Thank you so much. I'm new to this and didn't realise there was a code option.
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Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
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• 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
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by
GenoMax
141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
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Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
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Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
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3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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Are those 20% unaligned reads coming after hyper-editing detection?
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I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
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