Cuffdiff library types

Question

[fire_water]

Hello,

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.

Answer 1

[mastal511]

If you have Illumina paired-end data, then your reads are fr. Then you have to know if the library prep was unstranded or stranded.

[fire_water]

Thank you. If I have Illumina single-end data, then my reads are ff, correct?