Hello all i am new in field of genomics. recently i assembled my paired end RNA-seq data by trinity de novo assembler. Statistic asalysis showed that it produced 98343 contigs with the average mean length 875. Now i am confused either these are the unigenes too or i have to calculate by some other way. in various research paper they wrote for the determination of unigenes like this
Trinity Denovo assembly was carried out with short reads assembling programme Trinity, which first combined the reads with certain lengths of overlap to form longer fragments without ambiguous base know as contigs. *These contigs were than connected with Trinity to generate the sequence that could not be extended on either end. Such sequence were defined as Unigenes.*
i confused. is there any script in Trinity package that connected the contigs to generate the unigenes.
please help me in this regard. thanks