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Showing :
questions
0
votes
2
replies
2.4k
views
please share your experience for ORF prediction +blastp instead of doing blastx
blastp
ORF-prediction
blast
blastx
alignment
updated 2.8 years ago by
Ram
45k • written 9.7 years ago by
seta
★ 1.9k
7
votes
6
replies
7.5k
views
Gene ontology comparsion between up- and down-regulated genes
Gene ontology
differential expression
updated 8.6 years ago by
asanchez
▴ 20 • written 9.0 years ago by
seta
★ 1.9k
2
votes
3
replies
1.7k
views
Intron within the mRNA stranded-specific library
RNA sequencing
alternative splicing
updated 8.6 years ago by
harold.smith.tarheel
★ 5.0k • written 8.6 years ago by
seta
★ 1.9k
4
votes
4
replies
6.7k
views
Stranded-specific library by dUTP method
library
stranded-specific
dUTP
updated 8.6 years ago by
GenoMax
151k • written 8.6 years ago by
seta
★ 1.9k
0
votes
1
reply
1.8k
views
Annotation concept by BLAST2GO
alignment
blast
annotation
8.6 years ago by
seta
★ 1.9k
0
votes
7
replies
5.7k
views
How to calculate the average of mapping coverage?
read mapping
covergae
transcriptome
8.6 years ago by
seta
★ 1.9k
3
votes
4
replies
7.9k
views
Please help with "pheatmap" in R
pheatmap
log fold change
updated 8.6 years ago by
TriS
★ 4.8k • written 8.8 years ago by
seta
★ 1.9k
1
vote
1
reply
2.2k
views
Why longer K-mer is better for de novo assembly of high abundant transcript and vice versa?
transcript abundance
k-mer
assembly
updated 8.6 years ago by
iraun
6.2k • written 8.6 years ago by
seta
★ 1.9k
0
votes
1
reply
1.4k
views
What are the most important factors to get the full length contigs during de novo transcriptome assembly?
full length
de novo transcriptome assembly
updated 8.7 years ago by
Antonio R. Franco
★ 5.2k • written 8.7 years ago by
seta
★ 1.9k
1
vote
1
reply
2.8k
views
What is the main differences of pfam, ProDom and ProSiteProfiles?
domain protein database
pfma
prodom
8.7 years ago by
seta
★ 1.9k
11
votes
3
replies
4.5k
views
Finding UTR regions in the RNA sequencing data from a non-model organism
UTR
RNA-seq
non-model organism
updated 8.7 years ago by
EVR
▴ 610 • written 8.7 years ago by
seta
★ 1.9k
8
votes
3
replies
2.5k
views
Why the genome/transcriptome will be indexed before mapping
mapping
genome
index
transcriptome
updated 8.7 years ago by
ATpoint
88k • written 8.7 years ago by
seta
★ 1.9k
0
votes
0
replies
1.5k
views
Finding the transcript direction using stranded-specific library
RNA-seq
stranded-specific
assembly
8.7 years ago by
seta
★ 1.9k
2
votes
4
replies
5.6k
views
KOG/COG annotation results chart
chart KOG/COG annotation
alignment
updated 8.7 years ago by
Farbod
★ 3.4k • written 9.2 years ago by
seta
★ 1.9k
6
votes
19
replies
8.0k
views
Please help me with samtools
SAM
samtools
BAM
bowtie2
alignment
updated 2.8 years ago by
Ram
45k • written 9.6 years ago by
seta
★ 1.9k
0
votes
5
replies
5.0k
views
Please help with comparing several gene ontology (GO) list
Gene ontology
comparsion
differential expression
updated 8.8 years ago by
EagleEye
7.6k • written 8.8 years ago by
seta
★ 1.9k
0
votes
0
replies
2.0k
views
What are the advantages of domain homology search against KOG/COG database?
KOG/COG annotation
domain homology search
Blast
8.8 years ago by
seta
★ 1.9k
0
votes
0
replies
1.4k
views
CEGMA analysis, core gene or protein?
CEGMA analysis
core gene
assembly
8.9 years ago by
seta
★ 1.9k
1
vote
0
replies
2.5k
views
Regarding dispersion estimation of RNA-seq data by edgeR software
dispersion estimation
edgeR
8.9 years ago by
seta
★ 1.9k
2
votes
5
replies
3.0k
views
Why there is the same GO term in the both up- and down-regulated gene set?
differential expression analysis
GO term
RNA-seq
updated 8.9 years ago by
WouterDeCoster
48k • written 8.9 years ago by
seta
★ 1.9k
2
votes
6
replies
3.3k
views
Differentially expressed gene clustering
differentially expressed gene
clustering
updated 8.9 years ago by
Zhilong Jia
★ 2.2k • written 8.9 years ago by
seta
★ 1.9k
3
votes
10
replies
2.3k
views
Regarding differentially expressed genes analysis
RNA-Seq
differentially expressed genes
clustering
8.9 years ago by
seta
★ 1.9k
0
votes
0
replies
2.2k
views
Finding simple sequence repeat (SSR) markers for a specific disease
disease
simple sequence repeat
marker
Ilumina
8.9 years ago by
seta
★ 1.9k
0
votes
0
replies
1.6k
views
Please help me with the issue on FPKM value calculation and validation of transcriptome assembly
FPKM
assembly validation
qRT-PCR
updated 8.9 years ago by
Biostar
20 • written 9.1 years ago by
seta
★ 1.9k
6
votes
14
replies
6.3k
views
How to know the position of various transcripts of a given gene in the genomic sequence of that gene?
gene
transcript
sequence
position
updated 8.9 years ago by
Carlo Yague
9.0k • written 8.9 years ago by
seta
★ 1.9k
2
votes
2
replies
4.0k
views
ID conversion by BioMart
ID conversion
Ensembl
updated 9.0 years ago by
Denise CS
★ 5.2k • written 9.0 years ago by
seta
★ 1.9k
0
votes
4
replies
4.5k
views
KEGG enrichment analysis by BINGO plugin of Cytoscape
differential expression
KEGG enrichment analysis
9.0 years ago by
seta
★ 1.9k
6
votes
6
replies
13k
views
How to remove poly T in RNA-sequencing data
RNA-Seq
alignment
Assembly
sequencing
updated 2.5 years ago by
Ram
45k • written 10.0 years ago by
seta
★ 1.9k
5
votes
3
replies
3.7k
views
The best factors to evaluate the quality of de novo transcriptome assembly
sequencing
Assembly
RNA-Seq
updated 3.3 years ago by
Ram
45k • written 10.5 years ago by
seta
★ 1.9k
1
vote
1
reply
2.6k
views
Please advise on primer designing for qRT-PCR analysis of Trinity transcripts
Trinity
primer design
qRT-PCR
updated 9.2 years ago by
Biogeek
▴ 480 • written 9.2 years ago by
seta
★ 1.9k
0
votes
3
replies
8.7k
views
Why there is a big difference for blastn and blastx results of a given sequence
blast
alignment
sequence
updated 9.2 years ago by
Antonio R. Franco
★ 5.2k • written 9.2 years ago by
seta
★ 1.9k
0
votes
5
replies
3.6k
views
Venn diagram for annotation results
venn diagram
blast
annotation
updated 9.2 years ago by
Daniel
★ 4.0k • written 9.2 years ago by
seta
★ 1.9k
1
vote
2
replies
5.4k
views
blast against KOG database
blast
alignment
KOG annotation
updated 9.2 years ago by
Philipp Bayer
8.8k • written 9.2 years ago by
seta
★ 1.9k
0
votes
1
reply
2.9k
views
How to get required information from InterProscan results in xml format?
alignment
InterProscan
transcriptome
9.2 years ago by
seta
★ 1.9k
0
votes
3
replies
3.7k
views
Mapping of a de novo assembled transcriptome to a genome of relative species
genome
bowtie2
transcriptome-assembly
alignment
updated 2.8 years ago by
Ram
45k • written 9.6 years ago by
seta
★ 1.9k
0
votes
1
reply
3.1k
views
Running Interproscan on the cluster
interproscan
domain
Pfam
ProDomain
9.2 years ago by
seta
★ 1.9k
1
vote
4
replies
3.3k
views
Re-naming just part of header in fasta file
fasta
updated 2.2 years ago by
Ram
45k • written 9.3 years ago by
seta
★ 1.9k
6
votes
12
replies
4.4k
views
Plotting GO annotation results
GO annotation
transcriptome
Plotting
updated 9.3 years ago by
ivivek_ngs
★ 5.2k • written 9.3 years ago by
seta
★ 1.9k
0
votes
0
replies
3.8k
views
Pooling biological replicates and accuracy of differentially expressed genes analysis from RNA-seq experiment
gene-expression
biological-replicates
updated 2.9 years ago by
Ram
45k • written 9.3 years ago by
seta
★ 1.9k
0
votes
2
replies
2.7k
views
The best way to get the biologically meaningful interpretation from differentially expressed genes (DEG)
gene-ontology
DEG
transcriptome-assembly
updated 2.9 years ago by
Ram
45k • written 9.3 years ago by
seta
★ 1.9k
1
vote
1
reply
1.9k
views
Please suggest a suitable tool for GO annotation of a plant de novo assembled transcriptome
GO-analysis
annotation
updated 2.9 years ago by
Ram
45k • written 9.3 years ago by
seta
★ 1.9k
1
vote
2
replies
3.7k
views
The most popular GO annotation tool
gene-ontology
blastx
transcriptome-assembly
updated 2.9 years ago by
Ram
45k • written 9.4 years ago by
seta
★ 1.9k
0
votes
0
replies
2.1k
views
Uniquely mapped reads and differential expression analysis with Trinity
DEG-analysis
Trinity
mapping
updated 2.9 years ago by
Ram
45k • written 9.4 years ago by
seta
★ 1.9k
6
votes
23
replies
9.5k
views
6 follow
blast execution in linux
alignment
software-error
next-gen
blast
updated 3.2 years ago by
Ram
45k • written 10.4 years ago by
seta
★ 1.9k
0
votes
0
replies
1.8k
views
Zero coverage regions from mapping back reads to the transcriptome assembly
mapping
zero coverage
transcriptome assembly
9.4 years ago by
seta
★ 1.9k
1
vote
3
replies
5.0k
views
Contig length distribution plotting with R
contig
length
plotting
R
updated 9.5 years ago by
h.mon
35k • written 9.5 years ago by
seta
★ 1.9k
10
votes
18
replies
19k
views
8 follow
Please help with removing spaces from fasta file
fasta
updated 2.2 years ago by
Ram
45k • written 9.5 years ago by
seta
★ 1.9k
7
votes
18
replies
21k
views
How to check if there is any extra space or blank line in the fasta file?
fasta
updated 2.2 years ago by
Ram
45k • written 9.5 years ago by
seta
★ 1.9k
0
votes
4
replies
4.3k
views
Please help me with bowtie2 output and samtools report
bowtie2
samtools
flagstat
alignment
updated 2.9 years ago by
Ram
45k • written 9.5 years ago by
seta
★ 1.9k
0
votes
4
replies
3.2k
views
hit length in the tabular blast output
blast
hit length
tabular output
updated 9.5 years ago by
5heikki
11k • written 9.5 years ago by
seta
★ 1.9k
294 results • Page
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