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539 results • Page
1 of 11
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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 15 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 8 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
23 days ago by
b.contreras.moreira
▴ 170
4
votes
13
replies
857
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 8 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
matteo.levorato
• 0
2
votes
12
replies
729
views
Nanopore data filtering using fastp
fastp
nanopore
27 days ago by
emilydolivo97
▴ 10
3
votes
12
replies
490
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
23 days ago by
Lila M
★ 1.2k
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 29 days ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
2
votes
10
replies
820
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 27 days ago by
Ram
43k • written 9 weeks ago by
Sky
▴ 10
0
votes
10
replies
374
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
0
votes
10
replies
621
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
24 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 7 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
8
votes
10
replies
692
views
bash script
whole-genome-sequencing
updated 9 days ago by
Ram
43k • written 17 days ago by
bestone
▴ 30
0
votes
9
replies
477
views
Low number of both surviving reads after trimming
trimmomatic
trimming
27 days ago by
Jay
• 0
2
votes
9
replies
804
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
9
replies
578
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 13 days ago by
LauferVA
4.2k • written 14 days ago by
Aki
▴ 10
4
votes
9
replies
568
views
variant calling
variant-calling
updated 21 days ago by
Ram
43k • written 22 days ago by
dalibenam64
• 0
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 8 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
8
replies
283
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 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 15 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
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 7 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 20
0
votes
8
replies
520
views
STAR aligner options
STAR
28 days ago by
theophile
• 0
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 15 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
0
votes
7
replies
411
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 28 days ago by
GenoMax
141k • written 29 days ago by
Patadu94
• 0
0
votes
7
replies
398
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 20 days ago by
Papyrus
★ 2.9k • written 21 days ago by
doramora
▴ 10
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 15 days ago by
Ram
43k • written 6.4 years ago by
vikram
▴ 10
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq
WGCNA
removeBatchEffect
DESeq2
updated 8 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 16 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
7
replies
542
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
4
votes
7
replies
558
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 23 days ago by
cmdcolin
★ 3.8k • written 26 days ago by
I0110
▴ 140
1
vote
7
replies
888
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 29 days ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 8 days ago by
quentinperriere
• 0
2
votes
6
replies
860
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 8 days ago by
Ram
43k • written 19 months ago by
JACKY
▴ 140
0
votes
6
replies
613
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
differential-expression
RNA-Seq
ONT
Nanopore
updated 15 days ago by
Ram
43k • written 4 months ago by
tw_140
• 0
2
votes
6
replies
398
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
16 days ago by
jkim
▴ 170
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 1 day ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 15 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
5
votes
6
replies
391
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot
RNAseq
Rstudio
updated 22 days ago by
Istvan Albert
100k • written 23 days ago by
Pumla
• 0
0
votes
6
replies
548
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
9 days ago by
Dunois
★ 2.5k
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 15 days ago by
Ram
43k • written 5.7 years ago by
Pin.Bioinf
▴ 340
2
votes
6
replies
629
views
Overlapping and merging ChIP-seq peaks
MACS2
HOMER
ChIP-seq
peak-calling
updated 22 days ago by
Ram
43k • written 4 months ago by
zea
• 0
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 9 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 8 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
6
replies
456
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
15 days ago by
marongiu.luigi
▴ 710
4
votes
6
replies
832
views
bwa mem hangs after a few thousand reads
bwa
alignment
variant-calling
bwa-mem
updated 22 days ago by
Ram
43k • written 4 months ago by
cee28
▴ 30
0
votes
5
replies
275
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 8 days ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
0
votes
5
replies
198
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 20 hours ago by
GenoMax
141k • written 21 hours ago by
Bertalan_Takacs
▴ 90
0
votes
5
replies
398
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 14 days ago by
GenoMax
141k • written 15 days ago by
Shay
• 0
2
votes
5
replies
676
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by
Jesse
▴ 740 • written 5 days ago by
Ann
★ 2.4k
539 results • Page
1 of 11
Recent Votes
Answer: Figures are disappeared from html report of SnpEff
Comment: How to trim transcripts using information from NCBI contamination screen report
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
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Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
GenoMax
141k
At this point you should email NCBI help desk and ask them this question. If you get an answer then please post it back in this thread.
Comment: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff
by
analyst
▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data
by
Kazo
• 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
Answer: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
Answer: Finding orthologs between genome error
by
Adrian Altenhoff
★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid
by
ashaneev07
▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM
by
dsull
★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data
by
sehriban.buyukkilic
▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file
by
Pierre Lindenbaum
161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file
by
Maria
• 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
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