When you're interested in a genomic region, you can make use of RAD-seq data to investigate polymorphisms across Rhododendron. Instead of doing PCR and sequencing, you can find the sequence from genomic regions near a PstI restriction site (CTGCAG).
Data is loaded on the iMacs, see below for instructions. This will be similar to the RNA-seq from last week.
Open a Terminal window
cd RAD_seq
Add your sequence of interest in fasta format to input.fasta, then:
./blastn -query input.fasta -db all96.trimmed.spnames.fa -task blastn -outfmt 7
To get the sequence of the blast hit:
grep -A1 [SEQUENCENAME] all96.trimmed.spnames.fa
It's also possible to get several to many sequences at a time, let me know if you're interested in that.
Data is loaded on the iMacs, see below for instructions. This will be similar to the RNA-seq from last week.
Open a Terminal window
cd RAD_seq
Add your sequence of interest in fasta format to input.fasta, then:
./blastn -query input.fasta -db all96.trimmed.spnames.fa -task blastn -outfmt 7
To get the sequence of the blast hit:
grep -A1 [SEQUENCENAME] all96.trimmed.spnames.fa
It's also possible to get several to many sequences at a time, let me know if you're interested in that.
No comments:
Post a Comment