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1,013 results • Page
2 of 21
Sort: replies
Rank
Views
Votes
Replies
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
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
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
8
votes
10
replies
760
views
bash script
whole-genome-sequencing
updated 19 days ago by
Ram
43k • written 27 days ago by
bestone
▴ 30
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 25 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
9
votes
10
replies
480
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
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 18 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 18 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
1
vote
10
replies
992
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
10 days ago by
DKA
▴ 40
0
votes
10
replies
521
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 5 days ago by
i.sudbery
19k • written 12 days ago by
Patadu94
• 0
3
votes
10
replies
664
views
Piping samtools to R
R
NGS
bash
samtools
18 days ago by
noodle
▴ 580
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
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 5 days ago by
cwwong13
▴ 40 • written 6.7 years ago by
lessismore
★ 1.3k
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 18 days ago by
Ram
43k • written 2.0 years ago by
mmitra
▴ 60
1
vote
9
replies
4.7k
views
Help with multiple batch effects
sva
combat
batch-effect
updated 18 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
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic
Correlations
Python
Supergnova
Conda
updated 17 days ago by
Murat
• 0 • written 19 months ago by
Gerard
▴ 10
3
votes
9
replies
521
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 10 days ago by
Istvan Albert
100k • written 12 days ago by
Κοσμάς
• 0
3
votes
9
replies
895
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 17 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
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 6 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
1
vote
9
replies
568
views
Can index hopping lead to more reads in samples?
index-hopping
NovoSeq
illumina
NGS
Seqeucning
29 days ago by
Assa Yeroslaviz
★ 1.8k
9
votes
9
replies
516
views
High Malat-1 expression in single cell data
single-cell
updated 16 hours ago by
Ram
43k • written 6 days ago by
carolofharvest
▴ 30
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
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
2
votes
9
replies
896
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 11 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 18 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 22 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
0
votes
9
replies
630
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 23 days ago by
LauferVA
4.2k • written 24 days ago by
Aki
▴ 20
4
votes
8
replies
667
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 8 days ago by
Alex Reynolds
35k • written 9 days ago by
J
▴ 10
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 15 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna
RNA-Seq
ChIP-Seq
updated 27 days ago by
mflab
• 0 • written 3.9 years ago by
m.sadman.sakib
▴ 120
3
votes
8
replies
5.0k
views
An idea to identify batch effects
microarray
batch-effect
updated 16 days ago by
Ram
43k • written 9.7 years ago by
mjarosz
• 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 25 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
8
replies
437
views
What does it mean single base resolution in sequencing?
SNP
sequencing
updated 4 days ago by
LauferVA
4.2k • written 6 days ago by
jinyu
▴ 10
7
votes
8
replies
689
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
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
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
1
vote
8
replies
474
views
Downsampling fastq file
downsample
fastq
4 days ago by
marco.barr
▴ 90
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
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
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 2 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
6
votes
8
replies
609
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 18 days ago by
dariober
14k • written 20 days ago by
manaswiniparija3
▴ 40
0
votes
8
replies
395
views
Error in cnetplot enrichplot package
R
updated 12 days ago by
Ram
43k • written 12 days ago by
Farhad
• 0
1
vote
8
replies
896
views
Adding CB tag to bam file
samtools
bam
updated 10 days ago by
Pierre Lindenbaum
161k • written 16 days ago by
Maria
• 0
8
votes
8
replies
676
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 10 days ago by
swbarnes2
14k • written 11 days ago by
Aaliya
▴ 10
4
votes
7
replies
712
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 8 days ago by
dsull
★ 6.0k • written 12 days ago by
qudrat.nii
▴ 10
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 19 days ago by
george-hall-ucl
• 0 • written 9.3 years ago by
win
▴ 970
7
votes
7
replies
600
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein
pdb
protein-databank
updated 22 days ago by
Matthias Zepper
4.6k • written 22 days ago by
4fzcgueyp5
• 0
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 9 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
1,013 results • Page
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Recent Votes
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Comment: Raw counts using stringtie
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Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
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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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Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
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This the tool still problematic?
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Thank you for the advice, i'll keep that in mind.
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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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Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
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Thanujay S
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Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
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