Quick Start

From PileLine

Revision as of 14:21, 18 June 2010 (view source) Ggomez (Talk | contribs) ← Older edit		Revision as of 14:38, 18 June 2010 (view source) Ggomez (Talk | contribs) Newer edit →
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	:[[File:Case1Files.zip]]		:[[File:Case1Files.zip]]
	:[[File:Case2Files.zip]]		:[[File:Case2Files.zip]]
		+
		+	Each .zip file contains 2 pileup files:
		+	* Whole pileup file
		+	* Variants (vs reference genome) pileup file.
		+
		+	'''2.'''  You may compare Case1 vs Control1 at variant level using this command line:
		+
		+
		+
		+
		+
		+	: somatic mutations (Variants found in Case but not in Control)

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Revision as of 14:38, 18 June 2010

PipeLine input files

PileLine is capable to handle, filter and compare genomic position files (GP) including standard pileup, BED,GFF, or VCF files.

Basically, GP are tabular files where the two first columns contain chromosome name and position coordinate respectively. Additional optional fields may be added by users, see a GP file example below:

10     118829     optional1     optional2     optional3     ...    
10     121207     optional1     optional2     optional3     ...
10     121337     optional1     optional2     optional3     ...
10     121636     optional1     optional2     optional3     ...

PipeLine Guided example

1. Download GP example files (pileup format):

File:Control1Files.zip

File:Control2Files.zip

File:Case1Files.zip

File:Case2Files.zip

Each .zip file contains 2 pileup files:

• Whole pileup file
• Variants (vs reference genome) pileup file.

2. You may compare Case1 vs Control1 at variant level using this command line:

somatic mutations (Variants found in Case but not in Control)