PGAP - Revision history

Rf at 16:52, 6 May 2016

2016-05-06T16:52:06Z

Rf at 16:48, 6 May 2016

2016-05-06T16:48:19Z

Rf at 16:00, 6 May 2016

2016-05-06T16:00:04Z

Rf: /* Step 3 Running PGAP */

2016-05-06T15:46:31Z

‎Step 3 Running PGAP

Rf: Created page with "= Introduction = = Usage = == Step 3 Running PGAP == For PAGP, there are five functional modules: * cluster analysis of functional genes * pan-genome profile analysis * ge..."

2016-05-06T15:40:49Z

Created page with "= Introduction = = Usage = == Step 3 Running PGAP == For PAGP, there are five functional modules: * cluster analysis of functional genes * pan-genome profile analysis * ge..."

New page

= Introduction =

= Usage =

== Step 3 Running PGAP ==

For PAGP, there are five functional modules:
* cluster analysis of functional genes
* pan-genome profile analysis
* genetic variation analysis of functional genes
* species evolution analysis
* function enrichment analysis of gene clusters

The following commands could trigger all these
analysis modules with the default parameters.

← Older revision		Revision as of 16:52, 6 May 2016
Line 1:		Line 1:
	= Introduction =		= Introduction =
		+
		+	A perl based pipeline for clustering genes and ascertaining pan-genomes of prokaryotes.

	= Usage =		= Usage =

@@ Line 2: / Line 2: @@
 = Usage =
+'''PGAP.pl''' is the principle executable. Typing it without any arguments will give a helpful output.
 == Step 3 Running PGAP ==
@@ Line 17: / Line 17: @@
 The following commands trigger all these analysis modules with the default parameters.
   PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF

@@ Line 7: / Line 7: @@
 For PAGP, there are five functional modules:
-* functional genes into clusters
+* functional genes into clusters (invoked on commandline via '''--cluster''')
-* ascertain pan-genome profile
+* ascertain pan-genome profile (invoked on commandline via '''--pangenome''')
-* genetic variation of functional genes
+* genetic variation of functional genes (invoked on commandline via '''--variation''')
-* species evolution analysis
+* species evolution analysis (invoked on commandline via '''--evolution''')
-* function enrichment of gene clusters
+* function enrichment of gene clusters (invoked on commandline via '''--function''')
 Example command for this stage:
 The following commands trigger all these analysis modules with the default parameters.
-  PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster -pangenome --variation --evolution --function -method MP
+  PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF