spktornado / cas12f Goto Github PK

This project is about analysis Cas12f proteins.

a. Identify the Cas proteins.

a.1. Install the “prodigal.linux” , "bedtools" and “pilercr” in the default environment. prodigal.linux:https://github.com/yszhou2016/Cas13/tree/master/0.Cas-Finder bedtools: https://sourceforge.net/projects/bedtools/ pilecr: http://www.drive5.com/pilercr/

a.2. run “perl 0.Cas-Finder $sample.fasta” to obtain the Cas proteins and generate "$sample.pep.cas.fasta" file.

a.3. run " perl 1.Cas12f-Finder.pl $sample.pep.cas.fasta" to otain the Cas12f proteins and generate "$sample.pep.cas.Cas12.fa" file.

a.4. Multiple alignment of Cas12f proteins with mafft: mafft --maxiterate 1000 --thread 12 --globalpair Cas12f.fa > Cas12f.mafft.fasta

b. TracrRNA prediction.

run "perl 2.Cas12f.tracrRNA.Finder.pl Contig_name Cas12f_start Cas12f_end Direction CRISPR_array_start CRISPR_array_end Direct_repeat output" to obtain the potential tracrRNA and generate "*tracrRNA.txt" file.

c. Indel analysis. Install the “bwa” in the default environment.

run "perl 3.Indel_Calculate.pl Sample.R1.fastq Target_sequence Reference_sequence" and generate "*output.txt" file with Indel rate and Indel distrubution imformation.