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questions
9
votes
13
replies
5.6k
views
6 follow
converting paired end reads to single end, is this a good idea?
RNA-Seq
updated 15 months ago by
Ram
43k • written 6.3 years ago by
John
▴ 270
0
votes
0
replies
508
views
How to interpret exon ID?
rna-seq
exon
2.9 years ago by
John
▴ 270
2
votes
2
replies
1.4k
views
Google Cloud for RNA seq analysis
googlecloud
gcp
RNAseq
Cloud
updated 3.0 years ago by
GenoMax
142k • written 3.0 years ago by
John
▴ 270
0
votes
1
reply
1.4k
views
What number I should specify for SMARTer Stranded Total RNA-Seq Kit v2 for --forward-prob in RSEM?
RNA-Seq
rna-seq
updated 3.3 years ago by
tjbencomo
▴ 50 • written 4.4 years ago by
John
▴ 270
0
votes
1
reply
1.1k
views
How to get actual alignment % from STAR?
RNA-Seq
R
updated 4.2 years ago by
Biostar
20 • written 4.3 years ago by
John
▴ 270
14
votes
7
replies
13k
views
How to download mm10 GTF file with the gene id and gene name using UCSC table browser?
RNA-Seq
ucsc
alignment
updated 4.3 years ago by
Luis Nassar
▴ 650 • written 4.3 years ago by
John
▴ 270
13
votes
15
replies
6.5k
views
What % of rRNA contamination is acceptable?
RNA-Seq
rna-seq
alignment
updated 23 months ago by
Ram
43k • written 4.4 years ago by
John
▴ 270
2
votes
3
replies
2.7k
views
Why EBSEQ and DEseq2 gives different number of DE genes
RNA-Seq
rna-seq
R
alignment
gene
updated 4.6 years ago by
swbarnes2
14k • written 4.6 years ago by
John
▴ 270
22
votes
19
replies
4.8k
views
8 follow
edgeR gives no DE genes <0.05 FDR
R
RNA-Seq
software error
alignment
updated 4.6 years ago by
Antonio R. Franco
★ 5.1k • written 4.6 years ago by
John
▴ 270
10
votes
10
replies
12k
views
How to normalize my rna seq data?
RNA-Seq
Normalization
4.6 years ago by
John
▴ 270
5
votes
5
replies
1.6k
views
Is it necessary to do FastQC before using RSEM?
RNA-Seq
R
alignment
updated 4.7 years ago by
GenoMax
142k • written 4.7 years ago by
John
▴ 270
6
votes
7
replies
3.3k
views
How to create custom gtf annotation file?
RNA-Seq
R
genome
updated 4.8 years ago by
caggtaagtat
★ 1.9k • written 4.8 years ago by
John
▴ 270
1
vote
5
replies
959
views
How to Align only few transcript and get count?
RNA-Seq
R
rna-seq
next-gen
4.8 years ago by
John
▴ 270
9
votes
10
replies
1.7k
views
Differential network analysis for two treatments
RNA-Seq
R
4.8 years ago by
John
▴ 270
2
votes
2
replies
11k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
5.0 years ago by
John
▴ 270
6
votes
12
replies
7.9k
views
How to find correlation between two datasets/vectors?
RNA-Seq
5.1 years ago by
John
▴ 270
1
vote
5
replies
853
views
How much importance is RNAseq experimental bias?
RNA-Seq
rna-seq
sequence
sequencing
alignment
updated 5.1 years ago by
Devon Ryan
104k • written 5.1 years ago by
John
▴ 270
2
votes
10
replies
1.7k
views
Is there a way to compare single-cell RNA seq and Ribotag-seq?
RNA-Seq
rna-seq
next-gen
sequencing
gene
5.1 years ago by
John
▴ 270
0
votes
1
reply
1.6k
views
how to run RSEM with more paired end fastq files?
RNA-Seq
rna-seq
sequencing
R
updated 5.1 years ago by
h.mon
35k • written 5.1 years ago by
John
▴ 270
16
votes
8
replies
5.5k
views
How to combine multiple data files by column names?
RNA-Seq
rna-seq
R
updated 5.1 years ago by
zx8754
11k • written 5.1 years ago by
John
▴ 270
2
votes
3
replies
3.6k
views
How to perform Gene Set Enrichment Analysis for multiple treatments?
RNA-Seq
rna-seq
R
next-gen
sequencing
5.1 years ago by
John
▴ 270
3
votes
6
replies
1.4k
views
How to find cumulative gene score for gene list?
RNA-Seq
rna-seq
R
sequencing
gene
5.1 years ago by
John
▴ 270
4
votes
5
replies
6.0k
views
How to find differentially expressed genes between three groups?
RNA-Seq
rna-seq
ngs
r
R
updated 5.1 years ago by
daniele.avancini
▴ 70 • written 5.1 years ago by
John
▴ 270
2
votes
2
replies
2.2k
views
How can I show the group of gene's expression across Samples?
sequencing
RNA-Seq
r
rna-seq
5.1 years ago by
John
▴ 270
1
vote
1
reply
2.8k
views
Error: reduced dimension space doesn't match the dimension of the CellDataSet object?
RNA-Seq
sequence
R
software error
next-gen
updated 5.6 years ago by
Biostar
20 • written 6.2 years ago by
John
▴ 270
2
votes
4
replies
4.2k
views
what is residualModelFormulaStr in monocle?
r
R
RNA-Seq
software error
monocle
updated 6.0 years ago by
Batu
▴ 250 • written 6.2 years ago by
John
▴ 270
9
votes
4
replies
1.6k
views
How to determine the number of clusters in heirarchical clustering?
R
RNA-Seq
rna-seq
updated 6.0 years ago by
Biostar
20 • written 6.2 years ago by
John
▴ 270
0
votes
1
reply
792
views
How to check how many gene ontology terms sourced from manually curated versus electronic annotations?
RNA-Seq
rna-seq
r
R
updated 6.1 years ago by
Jean-Karim Heriche
27k • written 6.1 years ago by
John
▴ 270
0
votes
2
replies
1.5k
views
How to rank differentially expressed genes (output from EBSeq)?
R
RNA-Seq
rna-seq
6.1 years ago by
John
▴ 270
1
vote
4
replies
1.2k
views
How many samples suggested to perform differential gene expression analysis?
RNA-Seq
rna-seq
r
R
updated 6.1 years ago by
Nick
▴ 30 • written 6.1 years ago by
John
▴ 270
5
votes
6
replies
3.0k
views
How to perform gene ontology analysis with list of upregulated and down regulated genes?
RNA-Seq
rna-seq
r
updated 6.1 years ago by
taoi2
▴ 40 • written 6.1 years ago by
John
▴ 270
3
votes
4
replies
1.4k
views
How to delete the cells belongs to particlar CellType in R?
RNA-Seq
R
r
software error
updated 6.1 years ago by
Sean Davis
26k • written 6.1 years ago by
John
▴ 270
2
votes
1
reply
2.3k
views
How to fix (find) number of dimensions while reducing dimensions in tSNE method?
RNA-Seq
tsne
pca
rna-seq
R
6.1 years ago by
John
▴ 270
0
votes
0
replies
832
views
which algorithm used in classifyCells() function in Monocle?
RNA-Seq
R
rna-seq
sequencing
6.2 years ago by
John
▴ 270
0
votes
0
replies
3.8k
views
ERR: Perplexity is too large in Reducedimension step in Monocle
RNA-Seq
r
R
software error
6.2 years ago by
John
▴ 270
7
votes
4
replies
23k
views
how to sum up the columns to remove the duplicated row names in RSEM output?
R
RNA-Seq
updated 6.2 years ago by
Nicolas Rosewick
11k • written 6.2 years ago by
John
▴ 270
3
votes
6
replies
11k
views
How to overcome "duplicate row.names" error while importing tpm/count/fpkm matrix/table in R ?
R
software error
rna-seq
RNA-Seq
updated 6.2 years ago by
andrew.j.skelton73
6.6k • written 6.2 years ago by
John
▴ 270
0
votes
1
reply
2.0k
views
How to cluster single cell data using list of markers?
RNA-Seq
r
rna-seq
R
6.2 years ago by
John
▴ 270
0
votes
0
replies
956
views
How to find how many SRA bacterial transcriptome sequences are there in NCBI data base?
RNA-Seq
6.2 years ago by
John
▴ 270
1
vote
3
replies
2.8k
views
There is no gene information in RSEM output
rsem
RNA-Seq
rna-seq
updated 6.2 years ago by
Sean Davis
26k • written 6.2 years ago by
John
▴ 270
2
votes
1
reply
5.5k
views
How to get --transcript-to-gene-map <file> in RSEM?
rsem
RNA-Seq
reference
index
transcriptome
6.2 years ago by
John
▴ 270
0
votes
0
replies
1.6k
views
Subgrouping SIngle Cell in RNA-Seq Data Analysis
RNA-Seq
rna-seq
clustering
singlecell
6.3 years ago by
John
▴ 270
1
vote
3
replies
1.9k
views
Alternative for unsupervised clustering in scRNA Data
RNA-Seq
unsupervised clustering
gene expression
6.3 years ago by
John
▴ 270
5
votes
10
replies
2.9k
views
How to align mouse transcriptome data using bowtie2?
RNA-Seq
alignment
bowtie2
6.3 years ago by
John
▴ 270
1
vote
1
reply
2.6k
views
Can't I use STAR aligner in my laptop?
star
RNA-Seq
updated 6.3 years ago by
WouterDeCoster
47k • written 6.3 years ago by
John
▴ 270
15
votes
14
replies
3.2k
views
Penalty model of BWA MEM and BOWTIE2?
RNA-Seq
bwa mem
bowtie2
alignment
6.3 years ago by
John
▴ 270
14
votes
13
replies
17k
views
8 follow
BWA MEM vs BOWTIE2 , which is best?
bwamem
bowtie2
alignment
RNA-Seq
updated 6.3 years ago by
h.mon
35k • written 6.3 years ago by
John
▴ 270
0
votes
0
replies
821
views
alternative for molquest, for inter-operonic region finding
RNA-Seq
gene finder
6.3 years ago by
John
▴ 270
3
votes
6
replies
7.4k
views
bwa mem has more MAPQ values as 0 and 60
bwamem
bowtie2
6.3 years ago by
John
▴ 270
3
votes
3
replies
2.0k
views
How to calculate bowtie2 run time using python
RNA-Seq
bowtie2
alignment
python
updated 6.3 years ago by
Devon Ryan
104k • written 6.3 years ago by
John
▴ 270
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