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Old 02-08-2013, 11:56 AM   #1
anibhax
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Location: Pittsburgh

Join Date: Jan 2013
Posts: 24
Default NovoalignCS syntax help

Hi,

I'm having lot of trouble giving the right syntax for NovoalignCS. I have paired reads of SOLiD data and want to map them to human genome. I'm giving the following syntax and have no luck so far executing the tool.

novoalignCS
-d h19_index_novo_cs \
-f N12_0056_DefaultLibrary_F3.csfasta N12_0056_DefaultLibrary_F5-BC.csfasta N12_0056_DefaultLibrary_F3.QV.qual N12_0056_DefaultLibrary_F5-BC.QV.qual \
-F CSFASTAnQV \
-o SAM \
-i PE \
-k

The error it's displaying is: "Problem processing command line arguments: Unrecognised option. at N120056DefaultLibrary_F3.QV.qual".
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Old 10-31-2013, 10:38 PM   #2
sparks
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Location: Kuala Lumpur, Malaysia

Join Date: Mar 2008
Posts: 126
Default

Hi,

You do not need to specify the qual files on the command line, just the csfasta files. NovoalignCS will look for the qual files based on naming convention and use if found.

Colin
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