Download Discovery Environment Manual

Discovery Environment Manual
1
2
Getting Started
1.1
Accessing the Discovery Environment
5
1.2
Discovery Environment Overview
7
1.3
Manage Data
10
1.4
Perform Analyses
17
1.5
Viewing and Deleting Notifications
23
Analyses
2.1
Ancestral Character Estimation (ACE) Overview
26
2.2
Continuous Ancestral Character Estimation (CACE)
27
2.3
Discrete Ancestral Character Estimation (DACE)
32
2.4
Burrows-Wheeler Aligner Single End Reads
38
2.5
Burrows-Wheeler Aligner Paired End Reads
41
2.6
Cufflinks Transcript Quantification
44
2.7
FASTX Analyses Overview
49
2.8
FASTX Barcode Splitter (Single End)
50
2.9
FASTX Clipper
54
2.10 FASTX Quality Filter
59
2.11 FASTQ Quality Rescaler
62
2.12 FASTX Trimmer
65
2.13 Find SNPs Overview
68
2.14 Find SNPs
69
2.15 Independent Contrasts Overview
76
2.16 Independent Contrasts
77
2.17 Taxonomic Name Resolution Service (TNRS) Demo
83
2.18 TopHat Single End for Illumina
89
2.19 TopHat Paired End for Illumina
95