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1,032 results • Page
2 of 21
Sort: replies
Rank
Views
Votes
Replies
3
votes
10
replies
662
views
Piping samtools to R
R
NGS
bash
samtools
17 days ago by
noodle
▴ 580
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 19 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
9
votes
10
replies
462
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 2 days ago by
Zamin Iqbal
▴ 20 • written 3 days ago by
nicole.kavanagh
• 0
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 4 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
0
votes
10
replies
512
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 4 days ago by
i.sudbery
19k • written 12 days ago by
Patadu94
• 0
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 17 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 17 days ago by
Ram
43k • written 7.4 years ago by
linda
• 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 25 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 16 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
8
votes
10
replies
758
views
bash script
whole-genome-sequencing
updated 18 days ago by
Ram
43k • written 26 days ago by
bestone
▴ 30
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads
illumina
genome-assembly
updated 29 days ago by
Ram
43k • written 2.6 years ago by
predeus
★ 2.0k
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 20 days ago by
Aspire
▴ 330 • written 18 months ago by
Manav
• 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 17 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
1
vote
10
replies
987
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
9 days ago by
DKA
▴ 40
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 29 days ago by
Ram
43k • written 6.5 years ago by
J.F.Jiang
▴ 920
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 17 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
5 days ago by
anna
▴ 20
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 16 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
1
vote
9
replies
566
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
29 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 5 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 17 days ago by
Ram
43k • written 5.9 years ago by
fp89
▴ 30
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
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 21 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 1 day ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
9
votes
9
replies
484
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 1 day ago by
dsull
★ 6.0k • written 5 days ago by
carolofharvest
▴ 30
3
votes
9
replies
889
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 16 days ago by
Elisabeth Gasteiger
★ 2.4k • written 16 days ago by
Jacky
• 0
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 17 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
0
votes
9
replies
627
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 22 days ago by
LauferVA
4.2k • written 24 days ago by
Aki
▴ 20
2
votes
9
replies
895
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 10 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
3
votes
9
replies
515
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 10 days ago by
Istvan Albert
100k • written 11 days ago by
Κοσμάς
• 0
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray
batch-effect
updated 15 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 25 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 1 day ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
8
replies
392
views
Error in cnetplot enrichplot package
R
updated 11 days ago by
Ram
43k • written 11 days ago by
Farhad
• 0
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 26 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
0
votes
8
replies
579
views
FreeBayes encountered a sudden error
freebayes
updated 29 days ago by
Michael
54k • written 4 weeks ago by
emilydolivo97
▴ 10
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 24 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
1
vote
8
replies
709
views
6 follow
Finding insert sequences using long reads
insert-sequences
Nanopore
long-read-assembly
updated 25 days ago by
Anand Rao
▴ 630 • written 8 weeks ago by
bvm
▴ 20
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 14 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
7
votes
8
replies
683
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter
vcf
coverage
updated 22 days ago by
spen
▴ 40 • written 25 days ago by
MBarcelo
▴ 40
1
vote
8
replies
882
views
Adding CB tag to bam file
samtools
bam
updated 9 days ago by
Pierre Lindenbaum
161k • written 15 days ago by
Maria
• 0
6
votes
8
replies
604
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 17 days ago by
dariober
14k • written 19 days ago by
manaswiniparija3
▴ 40
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 17 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
4
votes
8
replies
655
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 7 days ago by
Alex Reynolds
35k • written 8 days ago by
J
▴ 10
8
votes
8
replies
667
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 9 days ago by
swbarnes2
14k • written 10 days ago by
Aaliya
▴ 10
0
votes
8
replies
436
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 3 days ago by
LauferVA
4.2k • written 5 days ago by
jinyu
▴ 10
1
vote
8
replies
469
views
Downsampling fastq file
downsample
fastq
4 days ago by
marco.barr
▴ 90
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 16 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
7
votes
8
replies
695
views
6 follow
How to BLAST more than 5 sequences against UniProt database?
BLAST
Protein
UniProt
29 days ago by
Riq
▴ 50
2
votes
7
replies
536
views
STARsolo ; Reads are NOT mapped to transcriptome
STARsolo
updated 23 days ago by
GenoMax
142k • written 25 days ago by
gdfsnkfns
• 0
1,032 results • Page
2 of 21
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I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
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Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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This the tool still problematic?
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I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
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You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
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The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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