User:Karmella Haynes/Notebook/PcTF Genomics/2014/04/02: Difference between revisions
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* Refer to [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/02/10 02/10/14] for the procedure and Command parameters | * Refer to [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2014/02/10 02/10/14] for the procedure and Command parameters | ||
* Refer to [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/19 12/19/11] for Hi-Seq parameters: fragment length (bioanalyzer result), read length | * Refer to [http://openwetware.org/wiki/User:Karmella_Haynes/Notebook/PcTF_Genomics/2011/12/19 12/19/11] for Hi-Seq parameters: fragment length (bioanalyzer result), read length | ||
* Input data must be | |||
* Example '''Command''' syntax: java -jar STAR.jar 100 1 true .5 10 true test_data1.txt false false test_out 1 true 10 5 0 | |||
{| {{table}} | {| {{table}} | ||
|- | |- | ||
| Parameter || | | Parameter || Command 1 | ||
|- | |- | ||
| Extension length || fragment length 200 - read length 100 = '''100''' | | Extension length || fragment length 200 - read length 100 = '''100''' | ||
|- | |||
| Start coordinate || 1 | |||
** Right end inclusion = '''true''' | ** Right end inclusion = '''true''' | ||
** FDR cut-off = '''.5''' | ** FDR cut-off = '''.5''' | ||
Revision as of 13:41, 2 April 2014
 Pc-TF Genomics
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04/02/14
STAR analysis
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