Mapping Transcriptome Reads To Est Database

Question

[Bdv]

hi I wnated to ask whether it makes sense to map transcriptome reads to est database or is it more reasonable to assemble without mapping to a reference in this case? Thank you

[Darked89]

ESTs from the same/related species or all species EST database?

[Bdv]

It is the same species.we are talking about a plant. What is the difference between ESTs and transcriptome sequencing?

Answer 1

[Darked89]

I do not think that mapping to unassembled and possibly highly redundant same species ESTs will help much. So if you want to map, then assemble ESTs first.

Also if possible, I will try to use ESTs for assembly, but it all depends how much variation there is between different strains/breeds etc. I.e. combining ESTs for highly polymorphic species like Ciona may give you more problems.

Answer 2

[Chris Evelo]

It would make more sense to map to an already existing assembled genome or Unigene like assembled mRNA database is that would be available. But of course that really depends on which species you are working with.

Answer 3

[Wind]

what software do you use to map short reads back to Unigenes?