[Bio-bwa-help] BWA problem eqnuiry?

[weilu <we...@cy...>]

Dear BWA user,

 

I am now using BWA to map my illumina read to reference genome. In the BWA
manual there is an option for 'aln' commond to trim reads. I use the option
as '. aln -q 30 .' But I always get the following problem. I couldn't get
more info from that manual. Do I use the command and option correctly?

>  

> [bwa_index] Construct SA from BWT and Occ... 0.02 sec [bwa_index] 

> Construct SA from reverse BWT and Occ... 0.04 sec

> aln: invalid option -- 'q'

> aln: invalid option -- 'q'

> [bwa_sai2sam_pe_core] convert to sequence coordinate...

>  

> Could you guys help me out with this program?

>  

> Best regards,

> Wei Lu

>  

> The University of Western Australia

> Faculty of Life & Physical Sciences

> School of Biomedical, Biomolecular & Chemical Sciences Discipline of 

> Microbiology & Immunology

>