Using blastn to look for intron/exons boundries

[alexa039]

Hi All
I am try to align RNAseq data to a genome to map the exons using blastn. The sequece alignment output terminates at the exact end of the alignment. I would like to see some additional bases at the end of the subject sequence so as to see where the GT/AG sequence is in the genomic sequence. I cant seem to see an option in the blastn manual. I saw some options such as best_hit_overhang but it didn't give the desired output.

Thanks in advance

[rdu]

I dont have an answer. Instead, I suggest you to switch your question to "Bioinformatics" section, because I can get replies soon after my questions being posted there. Good luck!

[alexa039]

thanks for the advice