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P4RNA_assembly
 The R scripts to assembly  Pol IV/RDR2-dependent transcripts

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Spliced_reads
 The scripts of identifying spliced reads

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count_Nu.pl
A perl function to calculate the number of sequences of each nucleotide  with nucleosomes for given coordinates
usage:
count_Nu.pl --file1 nucleosome_coor --file2 DNA_coor --size1 1000 --size2 200 -o output_Nu

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count_AT.pl
A perl function to calculate the number of A/T sequences of each nucleotide for given coordinates
usage:
count_AT.pl --file1 DNA_coor --file2 arabidopsis_whole_genome.fasta --size1 1000 --size2 200 -o output_AT 

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nucleosome_coor
The file contains some example position of nucleosome

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DNA_coor
The file contains some example coordinate in the genome 

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arabidopsis_whole_genome.fasta
The fasta file contains the genome sequences

