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518 results • Page
1 of 11
Sort: replies
Rank
Views
Votes
Replies
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma
differential-gene-expression
updated 17 days ago by
Ram
43k • written 5.0 years ago by
RNAseqer
▴ 260
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
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
24 days ago by
b.contreras.moreira
▴ 170
4
votes
13
replies
866
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 9 days ago by
BioinfGuru
★ 1.7k • written 15 days ago by
matteo.levorato
• 0
3
votes
12
replies
492
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
24 days ago by
Lila M
★ 1.2k
2
votes
12
replies
739
views
Nanopore data filtering using fastp
fastp
nanopore
29 days ago by
emilydolivo97
▴ 10
0
votes
11
replies
472
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
16 hours ago by
atowns21
• 0
8
votes
10
replies
699
views
bash script
whole-genome-sequencing
updated 10 days ago by
Ram
43k • written 18 days ago by
bestone
▴ 30
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 9 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
10
replies
824
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 29 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
0
votes
10
replies
623
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
25 days ago by
dzisis1986
▴ 70
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 8 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 9 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
480
views
Low number of both surviving reads after trimming
trimmomatic
trimming
28 days ago by
Jay
• 0
2
votes
9
replies
821
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 2 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
9
replies
580
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 14 days ago by
LauferVA
4.2k • written 16 days ago by
Aki
▴ 10
4
votes
9
replies
572
views
variant calling
variant-calling
updated 23 days ago by
Ram
43k • written 24 days ago by
dalibenam64
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 17 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
0
votes
8
replies
311
views
Error in cnetplot enrichplot package
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 16 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
0
votes
8
replies
524
views
STAR aligner options
STAR
29 days ago by
theophile
• 0
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 8 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
7
replies
241
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 hour ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 9 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 17 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
0
votes
7
replies
419
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 29 days ago by
GenoMax
141k • written 4 weeks ago by
Patadu94
• 0
0
votes
7
replies
399
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 21 days ago by
Papyrus
★ 2.9k • written 22 days ago by
doramora
▴ 10
4
votes
7
replies
560
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 24 days ago by
cmdcolin
★ 3.8k • written 28 days ago by
I0110
▴ 140
4
votes
7
replies
550
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 12 days ago by
Ram
43k • written 13 days ago by
AHerik
▴ 20
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 18 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
2
votes
7
replies
815
views
Removing duplicates
duplicates
ONT
minimap2
updated 7 days ago by
joe
▴ 510 • written 9 days ago by
quentinperriere
• 0
2
votes
6
replies
861
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 9 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 17 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
2
votes
6
replies
633
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 24 days ago by
Ram
43k • written 4 months ago by
zea
• 0
4
votes
6
replies
836
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 24 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
5
votes
6
replies
395
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 24 days ago by
Istvan Albert
100k • written 24 days ago by
Pumla
• 0
0
votes
6
replies
427
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 2 days ago by
gv
• 0 • written 25 days ago by
Srinka
▴ 20
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 9 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
6
replies
1.0k
views
Considering that the basal expression level is not 0 for the calculation of the differential expression
DESEQ2
RNA-Seq
Differential-gene-Expression
updated 17 days ago by
Ram
43k • written 5.7 years ago by
Pin.Bioinf
▴ 340
0
votes
6
replies
457
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
16 days ago by
marongiu.luigi
▴ 710
0
votes
6
replies
549
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
11 days ago by
Dunois
★ 2.5k
2
votes
6
replies
400
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
17 days ago by
jkim
▴ 170
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 10 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
0
votes
6
replies
615
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 17 days ago by
Ram
43k • written 5 months ago by
tw_140
• 0
0
votes
5
replies
333
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 21 days ago by
GenoMax
141k • written 22 days ago by
Sony
▴ 10
2
votes
5
replies
669
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 21 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
0
votes
5
replies
378
views
Parsing fasta file by coordinates
linux
fasta
updated 28 days ago by
GenoMax
141k • written 4 weeks ago by
sorrymouse
▴ 120
1
vote
5
replies
338
views
samtools filtering
samtools
updated 15 days ago by
jkbonfield
★ 1.2k • written 22 days ago by
sansan_96
▴ 80
3
votes
5
replies
409
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
updated 23 days ago by
GenoMax
141k • written 24 days ago by
e.r.zakiev
▴ 200
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 6 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
518 results • Page
1 of 11
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Answer: genome assembly records not present in assembly_summary.txt
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
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Comment: genome assembly records not present in assembly_summary.txt
Answer: genome assembly records not present in assembly_summary.txt
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Comment: PCA plot (Suggestions Needed)
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Recent Replies
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
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 aligning in regions wh…
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%d\…
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…
Answer: 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…
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