Bowtie - Mapping degradome to Transcriptome

[atulkakrana]

Hi All,

I have to use CleaveLand 3.0 for miRNA and target prediction but before I do so I need to map degradome to transcriptome using Bowtie v.2. My problem is that CleaveLand mentions:

"The cleaveland 3 scripts are meant to deal with mappings to the sense strand of transcriptome"

What does it actually means? We have the RNAseq data in our database but my confusion is that in db it matches with '+' and '-' of Rice genome. So is it that I have to use tags which are in '+' orientation and should rev. comp '-' strands before mapping by bowtie?

Or it doesn't matter to which strand in genome the 'tags' from RNAseq matches, it something to do with 'tag' orientation coming from RNAseq?

Expecting help.

AK

[giampe]

Hi,
I suggest you to try the PAREsnip tool, you can download a workbench version from http://srna-workbench.cmp.uea.ac.uk/tools/paresnip/
for my purpose it works fine!
I have also a question for you: do you have experience in sequencing degradome libraries constructed according German et al 2009?
we have a HiScan platform and we are planning to do a sequencing of degradome library, but we have doubts about which is the primer of sequencing to be used.
thanks