How to choose Tophat/Cufflinks Library Type for SOLiD data?

[mart555]

Hi all,
I have some unoriented data based on SOLiD 3 plus system, which Library Type should I choose when I running Tophat and Cufflinks?

Thanks！

[westerman]

I presume you are specifying these as '--single' reads. If so then I would put '-SS_lib_type' as 'F'.

[mart555]

yes, it is single reads, but I didn't find '--single' parameter in cufflinks and tophat?

[westerman]

My mistake. I was thinking of a different program other than tophat. Library type should be '
fr-secondstrand'