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Showing :
questions
6
votes
11
replies
16k
views
Convert HTSeq count table to RPKM value using GFF/GTF
tophat
RPKM
HTSeq
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Whoknows
▴ 960
1
vote
2
replies
2.1k
views
Software suggestion for RRBS DMR (methylation) analysis?
methylation
RRBS
next-gen
updated 3.8 years ago by
Shalu Jhanwar
▴ 520 • written 6.7 years ago by
Whoknows
▴ 960
7
votes
9
replies
5.7k
views
Tophat2 shows error during running
RNA-seq
Python
Tophat
updated 15 months ago by
Ram
43k • written 9.0 years ago by
Whoknows
▴ 960
1
vote
1
reply
1.8k
views
ROC for biomarker discovery
microarray
updated 6.8 years ago by
Samuel Brady
▴ 330 • written 6.9 years ago by
Whoknows
▴ 960
4
votes
1
reply
5.4k
views
How to filter mutect2 VCF output?
gatk
mutect2
SNP
alignment
updated 6.8 years ago by
poisonAlien
★ 3.2k • written 6.8 years ago by
Whoknows
▴ 960
65
votes
3
replies
295k
views
Understanding up and down regulated genes from LOG2 foldchange or foldchange
protein
gene-expression
RNA-Seq
updated 14 months ago by
Ram
43k • written 9.9 years ago by
Whoknows
▴ 960
3
votes
2
replies
2.1k
views
Urgent request - Pipeline for finding somatic and germline mutations of a cancer patient
exome
next-gen
SNP
updated 6.9 years ago by
TriS
★ 4.7k • written 6.9 years ago by
Whoknows
▴ 960
1
vote
3
replies
2.5k
views
How to find novel gene/isoform in 1 RNA-SEQ sample?
RNA-Seq
next-gen
updated 7.0 years ago by
EagleEye
7.5k • written 7.0 years ago by
Whoknows
▴ 960
0
votes
6
replies
2.5k
views
How to deal with RNA-SEQ samples with different number of raw reads?
RNA-Seq
alignment
updated 7.0 years ago by
Devon Ryan
104k • written 7.0 years ago by
Whoknows
▴ 960
0
votes
1
reply
2.1k
views
blastx strand in output file
strand
genome
sequence
blast
updated 7.4 years ago by
Tonor
▴ 480 • written 7.4 years ago by
Whoknows
▴ 960
1
vote
3
replies
2.3k
views
blastx output cut-off for creating gff
gff
blastx
ngs
7.4 years ago by
Whoknows
▴ 960
4
votes
11
replies
2.7k
views
How to visualize read depth based on genomic location
tophat
bed
bigwig
RNA-Seq
7.6 years ago by
Whoknows
▴ 960
6
votes
9
replies
4.6k
views
Unequal paired-end fastq size after quality control
RNA-Seq
fastq
Trimmomatic
updated 7.7 years ago by
mastal511
★ 2.1k • written 7.7 years ago by
Whoknows
▴ 960
3
votes
4
replies
3.8k
views
How to perform GO and Pathway analysis in plant?
RNA-Seq
alignment
protein
updated 7.7 years ago by
EagleEye
7.5k • written 7.7 years ago by
Whoknows
▴ 960
4
votes
5
replies
1.5k
views
R sharing code website for bioinformatics analysis
R
RNA-Seq
7.8 years ago by
Whoknows
▴ 960
0
votes
2
replies
1.1k
views
Protein family analysis
protein family
cluster
genome
sequence
Assembly
7.9 years ago by
Whoknows
▴ 960
1
vote
0
replies
1.3k
views
Downstream analysis for genome scaffold sequences (proteins)
uniprot
protein
fasta
genome
scaffold
7.9 years ago by
Whoknows
▴ 960
3
votes
2
replies
2.2k
views
Show sample genome on Jbrowse
jbrowse
fasta
gff
7.9 years ago by
Whoknows
▴ 960
33
votes
6
replies
11k
views
which one is better EdgeR or DEGSeq?
RNA-Seq
RPKM
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Whoknows
▴ 960
0
votes
0
replies
1.5k
views
How much reads really needs for de novo RNA-seq?
RNA-Seq
de novo
7.9 years ago by
Whoknows
▴ 960
3
votes
6
replies
3.1k
views
What is best commercial software for exome/genome interpretation?
ngs
exome
genome
updated 7.9 years ago by
Zaag
▴ 860 • written 7.9 years ago by
Whoknows
▴ 960
0
votes
0
replies
1.6k
views
"Not found" error in running gbrowse2 / gmod
ngs
gmod
gbrowse
fasta
7.9 years ago by
Whoknows
▴ 960
13
votes
15
replies
7.8k
views
8 follow
How to calculate average coverage for all genes
wig
bam
updated 13 months ago by
anii
• 0 • written 7.9 years ago by
Whoknows
▴ 960
0
votes
0
replies
1.2k
views
problem in running gbrowser2 / GMOD
gmod
gbrowse2
genome
NGS
7.9 years ago by
Whoknows
▴ 960
3
votes
12
replies
11k
views
bwa mem seq and Segmentation fault (core dumped)
bwa
genome
exome
8.1 years ago by
Whoknows
▴ 960
8
votes
5
replies
1.9k
views
Genome browser for website (ASP.net)
genome-browser
asp.net
variation
SNP
updated 21 months ago by
Ram
43k • written 8.3 years ago by
Whoknows
▴ 960
0
votes
1
reply
1.6k
views
How to treat with high mismatch reads in whole genome studies?
mismatch
sequencing
SNP
alignment
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Whoknows
▴ 960
3
votes
6
replies
4.5k
views
Finding isoform expression in RNA-Seq
tophat
isoform
RNA-Seq
cufflinks
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Whoknows
▴ 960
0
votes
4
replies
1.7k
views
Guidance for a personal medicine data center
SNP
genome
next-gen
personal-medicine
RNA-Seq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
Whoknows
▴ 960
0
votes
2
replies
2.1k
views
having up-regulated and down-regulated isoforms in Trinity output
RNA-Seq
Assembly
Trinity
updated 22 months ago by
Ram
43k • written 8.7 years ago by
Whoknows
▴ 960
3
votes
8
replies
5.5k
views
6 follow
Pathway analysis for transcriptome profiles
kegg
trinity
pathway
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.4 years ago by
Whoknows
▴ 960
1
vote
5
replies
3.0k
views
Error in samtools uniquely mapped reads file
Tophat
samtools
RNA-Seq
updated 2.1 years ago by
Ram
43k • written 9.2 years ago by
Whoknows
▴ 960
0
votes
5
replies
2.3k
views
Error in using repeat mask genome for tophat2
Tophat2
sequence
RNA-Seq
Assembly
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Whoknows
▴ 960
0
votes
0
replies
2.5k
views
Finding SSR marker in genome scale with comparison
DNA
genome
SSR
9.3 years ago by
Whoknows
▴ 960
2
votes
0
replies
3.6k
views
Futher analysis on Trinity fasta output
Assembly
trinity
RNA-Seq
updated 2.2 years ago by
Ram
43k • written 9.4 years ago by
Whoknows
▴ 960
0
votes
5
replies
2.9k
views
Problem in analyzing Rice RNA-Seq data
tophat
DESeq
HTSeq
cufflinks
DESeq2
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Whoknows
▴ 960
2
votes
1
reply
3.4k
views
Confusion in HTSeq paired-end output count
HTSeq
tophat
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Whoknows
▴ 960
4
votes
3
replies
3.7k
views
Sinking into the swamp by Using DESeq without replicates !!
HTSeq
DESeq
RNA-Seq
Tophat
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
Whoknows
▴ 960
2
votes
1
reply
2.5k
views
Normalization in DESeq
HTSeq
DESeq
RNA-Seq
Tophat
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
Whoknows
▴ 960
14
votes
5
replies
9.1k
views
Calculating RPKM for DESeq
RNA-Seq
HTSeq
DESEQ
Tophat
updated 13 months ago by
Chris
▴ 260 • written 9.7 years ago by
Whoknows
▴ 960
2
votes
1
reply
6.6k
views
Using HTSeq for paired-end files
HTSeq
DeSeq
RNA-Seq
Tophat
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
Whoknows
▴ 960
0
votes
4
replies
3.0k
views
Exact match in blastn
blastall
blastn
mismatch
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Whoknows
▴ 960
1
vote
0
replies
2.3k
views
Using Mireap for the Plant miRNA discovery
Mireap
Small-RNA
miRNA
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Whoknows
▴ 960
3
votes
5
replies
1.6k
views
1-based coordiante system for sam files
sam
bowtie
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Whoknows
▴ 960
15
votes
7
replies
5.9k
views
Finding significantly differentiall expressed genes in RNA-Seq with one sample
RNA-SEQ
p-value
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
Whoknows
▴ 960
0
votes
1
reply
3.0k
views
Bed file score , mismatch , and other column information
sam
miRNA
bowtie
bed
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
Whoknows
▴ 960
4
votes
10
replies
4.6k
views
How to create color range for RPKM/FPKM using R?
RNA-Seq
R
Graphic
ggplot2
gplots
10.0 years ago by
Whoknows
▴ 960
47 results • Page
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