Finding transcribed genes in R. williamsianum

Now that you know how to use BLAST on the command line, we can use it to look for interesting things.

Key among these are:
mRNA transcripts
RAD-sequencing from other species

I've put the necessary things on both new iMacs, and you can give it a try.

Open the file input.fasta, replace with your sequence in fasta format. Save the file.

Open Terminal.

cd RNA_seq

./blastn -query input.fasta -db Trinity_GG -task blastn -outfmt 7

Look over your blast hits. How many transcripts exist?

To get the fasta sequence of blast hits you're interested in:

python getFasta.py Trinity_GG.fa

Then paste in the sequence name, and copy out the result.