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1,129 results • Page
1 of 23
Sort: Views
Rank
Views
Votes
Replies
164
votes
70
replies
60k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
fastq
next-gen-sequencing
updated 28 days ago by
Ram
43k • written 12.8 years ago by
Panos
★ 1.8k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 17 days ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
87k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 9 days ago by
Ram
43k • written 6.7 years ago by
lessismore
★ 1.3k
103
votes
42
replies
31k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 17 days ago by
Jeremy Leipzig
22k • written 10.5 years ago by
14134125465346445
★ 3.6k
57
votes
22
replies
28k
views
7 follow
Batch correction in DESeq2
Combat
DESeq2
Batch-Effect
updated 20 days ago by
Ram
43k • written 4.5 years ago by
Arindam Ghosh
▴ 510
22
votes
14
replies
28k
views
7 follow
removing batch effects using ComBat and SVA
SVA
ComBat
R
Batch-effect
updated 17 days ago by
Ram
43k • written 7.9 years ago by
LJ
▴ 280
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 7 days ago by
kjngo
• 0 • written 12.0 years ago by
Gabriel R.
★ 2.9k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 8 days ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 7 days ago by
Hagen
▴ 10 • written 10.2 years ago by
filipzembol
▴ 180
81
votes
27
replies
20k
views
12 follow
ATAC-seq sample normalization
ChIP-Seq
atac-seq
normalization
updated 23 days ago by
sgv
• 0 • written 4.3 years ago by
Flo
▴ 240
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
1 day ago by
Kevin Blighe
87k
13
votes
13
replies
18k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna
protein
updated 18 days ago by
ummeswaiba
• 0 • written 10.3 years ago by
biostar
▴ 170
1
vote
7
replies
15k
views
7 follow
How To Annotate Methylation 450K?
methylation
updated 21 days ago by
Vassilis
• 0 • written 10.1 years ago by
liu4gre
▴ 210
17
votes
16
replies
14k
views
10 follow
How to extract the longest isoform from multi fasta file
perl
extract
fasta
python
isoform
updated 23 days ago by
Madeleine
• 0 • written 9.8 years ago by
jon.brate
▴ 310
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 16 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 8 days ago by
colindaven
6.4k • written 10.9 years ago by
Ontheway
▴ 10
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 41 minutes ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R
RNA-seq
edgeR
updated 16 days ago by
inedraylig
▴ 60 • written 2.9 years ago by
Pratik
★ 1.0k
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq
batch-effect
updated 7 days ago by
Ram
43k • written 7.4 years ago by
Tenghui Chen
• 0
17
votes
8
replies
12k
views
9 follow
MAF vs VAF
sequencing
updated 23 days ago by
AshleeThomson
▴ 80 • written 6.1 years ago by
lauren.wahyudi
▴ 50
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 16 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 29 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly
statistics
updated 13 days ago by
skdv2522
• 0 • written 4.7 years ago by
margab
▴ 10
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 9 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 9 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 5 days ago by
Ram
43k • written 10.6 years ago by
Louis
▴ 150
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 20 days ago by
Ram
43k • written 9.9 years ago by
midox
▴ 290
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 5 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 8 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 15 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 20 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 920
3
votes
6
replies
8.3k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 9 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
16
votes
10
replies
7.7k
views
6 follow
Intersect multiple BED files
bed
intersect
updated 29 days ago by
Alex Reynolds
35k • written 8.3 years ago by
int11ap1
▴ 470
4
votes
3
replies
7.6k
views
Genotype representation with 0, 1, 2 - what do they mean?
genotype
representation
phasing
imputation
gwas
updated 21 days ago by
far
• 0 • written 5.9 years ago by
Volka
▴ 180
4
votes
3
replies
7.4k
views
How to find/decipher Trimmomatic Output
trimmomatic
RNA-Seq
QC
updated 27 days ago by
Ram
43k • written 8.1 years ago by
nikelle.petrillo
▴ 110
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 9 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 15 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 10 days ago by
george-hall-ucl
• 0 • written 9.2 years ago by
win
▴ 970
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 1 day ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
9
votes
3
replies
7.0k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq
edgeR
Batch-Effect
updated 7 days ago by
Ram
43k • written 9.9 years ago by
Matina
▴ 250
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat
scRNA
batch-effect
harmony
updated 8 days ago by
Ram
43k • written 4.2 years ago by
623202215
▴ 80
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 7 days ago by
Ram
43k • written 4.5 years ago by
Lucy
▴ 140
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 9 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
0
votes
4
replies
6.5k
views
fastq-dump: command not found, what is wrong?
assembly
sratoolkit
genomics
updated 24 days ago by
spalmer
• 0 • written 2.7 years ago by
BioinfoNoob6
• 0
7
votes
20
replies
6.4k
views
7 follow
Repeat masked gtf files from ensembl
ensembl
RNA-Seq
genome
updated 15 days ago by
e.r.zakiev
▴ 200 • written 4.3 years ago by
kevin.stachelek
▴ 80
13
votes
10
replies
6.4k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression
RNA-Seq
Statistics
updated 16 days ago by
Ram
43k • written 5.7 years ago by
ucakhnd
▴ 40
3
votes
1
reply
6.2k
views
Normalization before or after merging the samples in Seurat
single-cell
seurat
batch-effect
updated 9 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID
org.Dr.eg.db
updated 9 days ago by
Ram
43k • written 5.5 years ago by
modarzi
▴ 170
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 7 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
12
votes
17
replies
6.0k
views
9 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 22 days ago by
Zuber
• 0 • written 3.9 years ago by
Eugene A
▴ 180
1,129 results • Page
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Comment: genome assembly records not present in assembly_summary.txt
Comment: genome assembly records not present in assembly_summary.txt
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Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely mapping in regions whe…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Pierre Lindenbaum
161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question
by
starswillfade
▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question
by
starswillfade
▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
Comment: genome assembly records not present in assembly_summary.txt
by
GenoMax
141k
Can you clarify what `metainfo` you are referring to? The accession that you refer to does exist in [**GenBank assembly_summary file**][1…
Comment: what is the purpose of indexing the reference genome (Kallisto)
by
i.sudbery
19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
benformatics
3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
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