These scripts have been developed for parsing the sam files of Net-Seq data, and extracting the information. Please see Imashimizu et al. 2015 for more details.
#Requirement
perl
#Usage
"count_error_bp.pl"
*Note: RNA base is complementary to the base detected in the NET-seq read.
$perl count_error_bp.pl -i [sam file] -l [read length] "parse_samtool_mpileup.pl"
$perl parse_samtool_mpileup.pl -i [pileupfile] -p [0.7] -d [0] "extractSequence.pl"
$perl extractSequence.pl -i [fasta] -peak [peak position file] -l [10] -comp [false] #Publication Imashimizu et al. Genome Biol. 2015 May 15;16(1):98.
#Author Hiroki Takahashi