After assembling of raw data i got 3 lakhs transcripts and now i want to separate unigenes from them. can suggest me how to separate them and tools used for unigenes identification ?
I am not sure what samples, data, organism etc. you are talking. If you have the .gff file containing the coordinates of your genes of interest then you could use BedTools suite to get the sequences in .fasta format (http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html) . Please be bit more clear as to what data you have and the organism etc.