Sequencing ssRNA virus using Bowtie

[sowmyai]

I am trying to assemble reads from an ssRNA virus into a reference genome. In this case, does strand bias apply ? Also, how should the second column of the Bowtie output "Reference strand(+/-) of the reference genome" be interpreted ? Should I discard all the - rows and only keep rows that align to the + strand of the reference ? Maybe I don't understand RNA and cDNA biology enough. Could someone please explain ?

[sowmyai]

One more question. Are Solexa paired-end read mates from the same or opposite strands ?

[Melissa]

Both strands can be sequenced. So do not discard the - strand. Somebody in the forum should be able to explain this better.