[maq-help] novo2maq

[Ryan M. <rm...@bc...>]

Has anyone else encountered problems running novo2maq on novoalign (unpaired) alignment files?  I have been running novoalign on individual lanes of data, and find that about 1 in 5 of my novoalign files cannot be converted into maq format.  I am getting the unhelpful "Segmentation Fault" message.  Is there any way to determine what might be causing this so I can rescue these alignment files?

Thanks,

Ryan