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Showing :
questions
7
votes
7
replies
3.7k
views
6 follow
Commercial Ngs Analysis Suites - Rate Them
next-gen
sequencing
analysis
software
written 13.0 years ago by
Travis
★ 2.8k
0
votes
7
replies
2.1k
views
Tophat2/Bowtie failing to align some examples of partial intron retention / exon loss
RNA-Seq
alignment
updated 5.8 years ago by
Charles Warden
8.3k • written 5.8 years ago by
Travis
★ 2.8k
17
votes
12
replies
5.0k
views
7 follow
Has Anyone Tried Rum For Aligning/Counting Illumina Rna-Seq Data?
rna
alignment
updated 6.3 years ago by
Biostar
20 • written 13.2 years ago by
Travis
★ 2.8k
61
votes
27
replies
28k
views
18 follow
Links To Good Next Gen Sequence Analysis Training Courses And Centres
next-gen
sequencing
analysis
workshops
training
updated 2.5 years ago by
Ram
44k • written 13.2 years ago by
Travis
★ 2.8k
3
votes
14
replies
6.8k
views
Problems With Bioconductor'S Genomicfeatures Package
r
bioconductor
next-gen
sequencing
rna
updated 8.0 years ago by
Stephane Plaisance
▴ 460 • written 13.1 years ago by
Travis
★ 2.8k
11
votes
5
replies
4.8k
views
Genomic Alignment And Snp/Indel Calling - My First Ever "Pipeline"
snp
indel
next-gen
sequencing
updated 8.7 years ago by
Biostar
20 • written 13.4 years ago by
Travis
★ 2.8k
4
votes
8
replies
4.2k
views
Bwa Aln For Snp/Indel Discovery With Paired End 100Bp Human Dna Reads
bwa
dna
next-gen
sequencing
snp
indel
updated 8.7 years ago by
Biostar
20 • written 13.4 years ago by
Travis
★ 2.8k
1
vote
4
replies
4.2k
views
Vcf Files With (Simulated) Phenotypes For Association Studies
association
vcf
next-gen
sequencing
simulation
updated 8.8 years ago by
Biostar
20 • written 12.6 years ago by
Travis
★ 2.8k
6
votes
21
replies
7.7k
views
Problem Installing Bioconductor "Goseq" Package
bioconductor
rna
next-gen
sequencing
r
updated 2.3 years ago by
Ram
44k • written 12.9 years ago by
Travis
★ 2.8k
3
votes
1
reply
2.9k
views
Good Resource To Learn About 'Smaller' De Novo Eukaryotic Genome Assembly
next-gen
sequencing
denovo
assembly
genome
updated 9.6 years ago by
Biostar
20 • written 12.7 years ago by
Travis
★ 2.8k
100
votes
12
replies
38k
views
14 follow
Best Software For Detection Of Somatic Mutations From Matched Tumor:Normal Ngs Data
somatic-mutation
variant-calling
SNV
updated 3.0 years ago by
Ram
44k • written 12.5 years ago by
Travis
★ 2.8k
3
votes
6
replies
3.4k
views
Srma (Short Read Micro-Aligner) Optimising For Speed
short
alignment
snp
next-gen
sequencing
updated 10.3 years ago by
Biostar
20 • written 13.3 years ago by
Travis
★ 2.8k
0
votes
4
replies
3.9k
views
Rna-Seq And Multivariate Classifiers
next-gen
sequencing
classification
rna
updated 10.5 years ago by
Biostar
20 • written 13.1 years ago by
Travis
★ 2.8k
0
votes
3
replies
3.7k
views
Comparing Rpkms For One Test Sample Vs Multiple Controls
rna-seq
differential-expression
next-gen
updated 10.9 years ago by
Hayssam
▴ 280 • written 10.9 years ago by
Travis
★ 2.8k
18
votes
8
replies
11k
views
7 follow
Introducing Known Mutations (From A Vcf) Into A Fasta File
mutation
vcf
fasta
next-gen
sequencing
updated 11.3 years ago by
Ashutosh Pandey
12k • written 12.6 years ago by
Travis
★ 2.8k
14
votes
10
replies
4.7k
views
Using Simngs To Generate Reads
next-gen
sequencing
read
simulation
illumina
updated 11.4 years ago by
guillemch
▴ 140 • written 13.4 years ago by
Travis
★ 2.8k
4
votes
4
replies
3.7k
views
Illumina Ngs Test Data For Snp/Indel Calling And Association Study
next-gen
sequencing
snp
association
updated 11.4 years ago by
marcodpc
▴ 60 • written 13.4 years ago by
Travis
★ 2.8k
2
votes
3
replies
4.0k
views
Database Of Human Structural Variants Enabling Vcf File Creation
next-gen
vcf
sv
updated 12.2 years ago by
deanna.church
★ 1.1k • written 12.2 years ago by
Travis
★ 2.8k
26
votes
30
replies
13k
views
9 follow
Trying To Understand A Simple Perl Vs Python Vs Sed Benchmark
perl
python
updated 12.4 years ago by
Marvin
▴ 900 • written 12.4 years ago by
Travis
★ 2.8k
11
votes
3
replies
4.7k
views
Filtering Ngs Genomic Alignments
next-gen
sequencing
alignment
filter
paired
updated 12.6 years ago by
John St. John
★ 1.2k • written 13.4 years ago by
Travis
★ 2.8k
3
votes
10
replies
5.9k
views
Large Deletions With Bwa And Single End Reads
indel
next-gen
sequencing
alignment
bwa
updated 12.6 years ago by
Ying W
★ 4.3k • written 12.8 years ago by
Travis
★ 2.8k
12
votes
4
replies
3.1k
views
Does Anyone Know Of A Publication Reviewing Snp/Indel Finding Algorithms For Ngs Data?
next-gen
sequencing
snp
indel
publication
updated 12.6 years ago by
Thomas
▴ 760 • written 13.2 years ago by
Travis
★ 2.8k
2
votes
5
replies
3.2k
views
Software To Simulate Solid Colorspace Reads
simulation
next-gen
sequencing
solid
updated 12.6 years ago by
Drio
▴ 920 • written 13.2 years ago by
Travis
★ 2.8k
2
votes
8
replies
5.3k
views
Confused By Wgsim Output
next-gen
sequencing
short
samtools
12.6 years ago by
Travis
★ 2.8k
7
votes
6
replies
3.1k
views
Read Generator With Clear Annotation Of Read Origin And Mutations
short
next-gen
sequencing
simulation
alignment
updated 12.6 years ago by
Pierre Lindenbaum
164k • written 13.2 years ago by
Travis
★ 2.8k
153
votes
32
replies
9.2k
views
23 follow
Picking A Programming Language And Where To Begin
programming
next-gen
sequencing
c
subjective
updated 12.7 years ago by
Palani Kannan
▴ 60 • written 13.2 years ago by
Travis
★ 2.8k
2
votes
2
replies
2.6k
views
Using Bfast To Align Illumina Paired End Reads
next-gen
sequencing
alignment
updated 12.8 years ago by
brentp
24k • written 12.8 years ago by
Travis
★ 2.8k
4
votes
5
replies
4.5k
views
Samtools Mpileup And Bcftools Calling Snps Againt Non-Existent N Characters
next-gen
sequencing
samtools
snp
bcftools
updated 12.9 years ago by
Swbarnes2
★ 1.6k • written 12.9 years ago by
Travis
★ 2.8k
2
votes
12
replies
4.1k
views
Bioconductor Problem With Maketranscriptdbfrombiomart (Genomicfeatures Package)
r
rna
bioconductor
next-gen
sequencing
updated 12.9 years ago by
Jeremy Leipzig
22k • written 12.9 years ago by
Travis
★ 2.8k
17
votes
4
replies
5.1k
views
Rna-Seq Transcript Length Bias - Is There A 'Standard' Approach To Accounting For It
rna
data
next-gen
sequencing
updated 12.9 years ago by
seidel
11k • written 12.9 years ago by
Travis
★ 2.8k
1
vote
2
replies
1.9k
views
Using Platform Lsf To Parallelize Basic Bioinformatics Tasks
parallel
alignment
updated 13.0 years ago by
Sean Davis
27k • written 13.0 years ago by
Travis
★ 2.8k
11
votes
4
replies
6.7k
views
Exon Arrays Vs Rna-Seq
rna
next-gen
sequencing
exon
updated 13.0 years ago by
Malachi Griffith
20k • written 13.0 years ago by
Travis
★ 2.8k
3
votes
5
replies
2.9k
views
Is Association Testing With Mpileup A Sound Approach?
next-gen
sequencing
samtools
association
plink
genetics
updated 13.1 years ago by
Larry_Parnell
16k • written 13.1 years ago by
Travis
★ 2.8k
22
votes
7
replies
7.8k
views
Differential Expression Analysis Theory/Tutorial For The Statistics Layman
rna
gene
next-gen
sequencing
statistics
13.1 years ago by
Travis
★ 2.8k
12
votes
5
replies
3.8k
views
Is Anyone Familiar With Knome And Their Kgap Software?
next-gen
sequencing
genome
exome
analysis
updated 13.1 years ago by
Nathan Pearson
▴ 10 • written 13.2 years ago by
Travis
★ 2.8k
7
votes
13
replies
8.0k
views
Single Gene Sequencing And Mutation Analysis
sanger
snp
structural
next-gen
sequencing
alignment
updated 13.2 years ago by
Leonor Palmeira
3.9k • written 13.2 years ago by
Travis
★ 2.8k
36
votes
4
replies
7.5k
views
Variation & Genotype Calling From Ngs Data - Per Sample Or Multi Sample?
snp
variation
next-gen
sequencing
updated 13.2 years ago by
lh3
33k • written 13.2 years ago by
Travis
★ 2.8k
12
votes
7
replies
4.5k
views
Benchmarking Read Alignment And Variant-Calling Algorithms (For Dummies)
alignment
snp
indel
algorithm
updated 13.2 years ago by
Torst
▴ 980 • written 13.2 years ago by
Travis
★ 2.8k
11
votes
9
replies
9.2k
views
Illlumina Paired End Reads File Format
next-gen
sequencing
paired
updated 13.2 years ago by
Sean Davis
27k • written 13.4 years ago by
Travis
★ 2.8k
35
votes
11
replies
11k
views
8 follow
Thoughts On Galaxy For Next Generation Sequence Data Analysis
next-gen
sequencing
galaxy
updated 13.2 years ago by
Mohammed Shomam
• 0 • written 13.2 years ago by
Travis
★ 2.8k
11
votes
4
replies
5.5k
views
Has Anyone Heard Of Noiseq? A New Method For Differential Expression Analysis.
rna
next-gen
sequencing
updated 13.2 years ago by
seidel
11k • written 13.2 years ago by
Travis
★ 2.8k
14
votes
8
replies
7.1k
views
6 follow
Using Cufflinks For Rna-Seq Without Tophat/Bowtie.
rna
alignment
updated 13.2 years ago by
Gww
★ 2.7k • written 13.2 years ago by
Travis
★ 2.8k
5
votes
5
replies
5.3k
views
How Do You Do Local Realignment Around Indels For Exome Sequencing?
snp
indel
next-gen
sequencing
alignment
mapping
updated 13.3 years ago by
Docroberson
▴ 310 • written 13.3 years ago by
Travis
★ 2.8k
20
votes
4
replies
6.7k
views
Bioconductor/R For Ngs Analysis
next-gen
sequencing
bioconductor
r
updated 13.3 years ago by
Chris Evelo
10k • written 13.3 years ago by
Travis
★ 2.8k
16
votes
13
replies
15k
views
How To Build A Basic Rna-Seq Pipeline
next-gen
sequencing
rna
gene
updated 13.3 years ago by
Radhouane Aniba
▴ 790 • written 13.3 years ago by
Travis
★ 2.8k
6
votes
5
replies
5.3k
views
Next Gen Sequencing Indel Realignment With The Genome Analysis Toolkit (Gatk)
alignment
indel
snp
gatk
next-gen
sequencing
updated 13.4 years ago by
Ian
6.1k • written 13.4 years ago by
Travis
★ 2.8k
14
votes
15
replies
7.1k
views
Paired-End Sequence Preprocessing Effects On Downstream Processes
next-gen
sequencing
alignment
paired
updated 13.4 years ago by
Mitch Bekritsky
★ 1.3k • written 13.4 years ago by
Travis
★ 2.8k
32
votes
5
replies
5.5k
views
Defining Your Reference Genome From Ucsc For Human Ngs Studies
next-gen
sequencing
genome
reference
updated 13.4 years ago by
lh3
33k • written 13.4 years ago by
Travis
★ 2.8k
16
votes
21
replies
5.3k
views
6 follow
Bfast And Mpileup - How Time Consuming?
samtools
snp
hardware
13.4 years ago by
Travis
★ 2.8k
11
votes
7
replies
7.3k
views
Ngs Dna Read Simulator With Quality Scores Available?
simulation
dna
next-gen
sequencing
samtools
quality
updated 13.4 years ago by
Mitch Bekritsky
★ 1.3k • written 13.4 years ago by
Travis
★ 2.8k
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