Cuffdiff BAM record error

I am continuing the “Genomic Data Science” course from Coursera. However, I have to use Cufflink-Cuffmerge-Cuffdiff sequentially to perform differential expression analysis that existed last week. Cufflink and Cuffmerge work fine, but whatever I tried Cuffdiff failed. I could not understand why this is so.

BAM record error: found spliced alignment without XS attribute

I get this error line.

I think it can be solved by setting the Library prep used for input reads to ff-firststrand. To see this option you need to set parameter Set Advanced Cuffdiff parameters? to yes.

I am not sure what it exactly does but then at least you have a starting point to solve it. Hopefully a more experienced user can give an better answer.