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539 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 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
22 days ago by
b.contreras.moreira
▴ 170
4
votes
13
replies
855
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
725
views
Nanopore data filtering using fastp
fastp
nanopore
27 days ago by
emilydolivo97
▴ 10
3
votes
12
replies
488
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
22 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
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
8
votes
10
replies
692
views
bash script
whole-genome-sequencing
updated 9 days ago by
Ram
43k • written 16 days ago by
bestone
▴ 30
0
votes
10
replies
619
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
23 days ago by
dzisis1986
▴ 70
0
votes
10
replies
363
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
819
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
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
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
797
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
577
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
280
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 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
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
0
votes
8
replies
518
views
STAR aligner options
STAR
27 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 7 days ago by
Ram
43k • written 7.0 years ago by
tud55122
▴ 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
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
411
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 28 days ago by
GenoMax
141k • written 28 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 8 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
4
votes
7
replies
540
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
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
0
votes
7
replies
397
views
DESeq: too low p-value for RNAseq
R
DESeq
p-value
RNA-seq
FDR
updated 19 days ago by
Papyrus
★ 2.9k • written 20 days ago by
doramora
▴ 10
2
votes
7
replies
805
views
Removing duplicates
duplicates
ONT
minimap2
updated 6 days ago by
joe
▴ 510 • written 7 days ago by
quentinperriere
• 0
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
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
2
votes
6
replies
397
views
create a gene count matrix csv file from seurat object
Seurat
sparseMatrix
16 days ago by
jkim
▴ 170
2
votes
6
replies
859
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
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
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
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
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
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
5
votes
6
replies
390
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
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 22 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
0
votes
6
replies
547
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
9 days ago by
Dunois
★ 2.5k
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
6
replies
452
views
Error in running Mauve alignner in Ubuntu 20.04
java
linux
aligner
mauve
15 days ago by
marongiu.luigi
▴ 710
2
votes
5
replies
668
views
samtools mpileup taking too long
Bam
samtools
sam
alignment
updated 19 days ago by
Ram
43k • written 6 weeks ago by
K
• 0
0
votes
5
replies
485
views
How to assure that sequence consensus is genuine?
genome
18 days ago by
marongiu.luigi
▴ 710
1
vote
5
replies
335
views
samtools filtering
samtools
updated 13 days ago by
jkbonfield
★ 1.2k • written 21 days ago by
sansan_96
▴ 80
0
votes
5
replies
325
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 20 days ago by
GenoMax
141k • written 20 days ago by
Sony
▴ 10
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
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
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Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
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b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
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• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
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by
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• 0
Thank you so much. Should i proceed for annotation step?
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14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
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Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
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JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
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Aaliya
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I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
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So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
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by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
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Kevin Blighe
87k
You will have to elaborate on what is the error
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▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
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duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
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Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
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14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
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