The Velvet manual documents a "strand_specific" argument for transcriptome assembly. If this option is specified, how does the assembler ascertain the strand that a read comes from? My guess would be it looks for a trailing "/1" or "/2". Can anyone confirm this or give me a better answer. Here is what the Velvet Manual has to say on the issue:
"Strand speciﬁc sequencing
If you are using a strand speciﬁc transcriptome sequencing protocol, you may
wish to use this option for better results. Even though it can be used anywhere
on the command line, it applies to all the dataset. To toggle it on, type:
./velveth output_directory/ 21 (...data files...) -strand_specific"