Is there a simple way to determine if a given SFF file contains data for Paired End (PE) or Single end (SE) reads?
I guess I could try matching the standard linker sequence to some of the reads, but it would be nice if the information were directly readable from the file. I tried looking at the manifest using sffinfo, but their was nothing there that suggested PE or not PE.
I found that if I run the SFF through gsMapper, it will create ACCNO_left and ACCNO_right version of the reads, representing the left and right ends of a given PE read. However, its a pain to run all my SFF's through gsMapper just to determine which ones it (somehow) determines to be PE.
If I ran SSAHA2 to find the linker, for example, what would be the command line?
Is their a better tool to choose?
Sorry for the Noobs...
Cheers,
I guess I could try matching the standard linker sequence to some of the reads, but it would be nice if the information were directly readable from the file. I tried looking at the manifest using sffinfo, but their was nothing there that suggested PE or not PE.
I found that if I run the SFF through gsMapper, it will create ACCNO_left and ACCNO_right version of the reads, representing the left and right ends of a given PE read. However, its a pain to run all my SFF's through gsMapper just to determine which ones it (somehow) determines to be PE.
If I ran SSAHA2 to find the linker, for example, what would be the command line?
Is their a better tool to choose?
Sorry for the Noobs...
Cheers,
Comment