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
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
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