I was wondering if someone could help me understand the different library types in Cuffdiff. I noticed that when I view the man page in Terminal it lists the following supported library types:
ff-firststrand ff-secondstrand ff-unstranded fr-firststrand fr-secondstrand fr-unstranded (default) transfrags
However, when I visit the online documentation it only describes the fr-* options, not the ff-* options.
If it helps, the data I will be feeding to Cuffdiff is a result of Bowtie1, then sorting, indexing, and converting into BAM format. The original FASTQ files were in Sanger / Illumina 1.9 format.
Thanks a lot.