Novoaligncs Syntax Help

Question

[Jordan]

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 N12_0056_DefaultLibrary_F3.QV.qual".

Answer 1

[Ashutosh Pandey]

Can you give a link to the manual ? I think the csfasta and the qual file for each pair should go together (one after the other). Sth like

-f N12_0056_DefaultLibrary_F3.csfasta N12_0056_DefaultLibrary_F3.QV.qual N12_0056_DefaultLibrary_F5-BC.csfasta  N12_0056_DefaultLibrary_F5-BC.QV.qual