需要準備的資料：
降解組測序資料QC後整理為redundant fasta格式
轉錄本資料，fasta格式
miRNA序列，fasta格式

檢視幫助文件

CleaveLand4.pl --help

readscount轉為fasta格式(redundent reads)

從NCBI下載的測序資料很多是去過接頭的，並且整理成readscount格式，即每行第一列為reads，第二列為reads數，而我們需要把它整理成fasta格式，並且每個read都整理為一條序列

執行CleaveLand

mode 1

CleaveLand4.pl -e GSM3124755_WTB_PARE.fas -u Ath_MITE-miRNA_mature.fas -n Athaliana_167_TAIR10.cds_primaryTranscriptOnly.fa -o plot/ > GSM3124755_WTB_PARE.out

-e 降解組測序reads，fasta格式
-u miRNA序列，fasta格式
-n 轉錄本資料，fasta格式
-o 指定資料夾，輸出降解組圖
 

幾種模式

Usage: CleaveLand4.pl [options] > [out.txt]
Options:
-h Print help message and quit
-v Print version and quit
-q Quiet mode … no log/progress information to STDERR
-a Sort small RNA / transcript alignments by Allen et al. score instead of default MFEratio – for GSTAr
-t Output in tabular format instead of the default verbose format
-r [float >0…1] Minimum Free Energy Ratio cutoff. Default: 0.65 – for GSTAr
-o [string] : Produce T-plots in the directory indicated by the string. If the dir does not exist, it will be
created
-d [string] : Path to degradome density file.
-e [string] : Path to FASTA-formatted degradome reads.
-g [string] : Path to GSTAr-created tabular formatted query-transcript alignments.
-u [string] : Path to FASTA-formatted small RNA queries
-n [string] : Path to FASTA-formatted transcriptome
-p [float >0…1] : p-value for reporting. Default is 1 (no p-value filtering).
-c [integer 0…4] : Maximum category for reporting. Default is 4 (all categories reported).

1. Align degradome data, align small RNA queries, and analyze.
   REQUIRED OPTIONS: -e, -u, -n
   DISALLOWED OPTIONS: -d, -g
2. Use existing degradome density file, align small RNA queries, and analyze.
   REQUIRED OPTIONS: -d, -u, -n
   DISALLOWED OPTIONS: -e, -g
3. Align degradome data, use existing small RNA query alignments, and analyze.
   REQUIRED OPTIONS: -e, -n, -g
   DISALLOWED OPTIONS: -d, -u
   IRRELEVANT OPTIONS: -a, -r
4. Use existing degradome density file and existing small RNA query alignments, and analyze.
   REQUIRED OPTIONS: -d, -g
   DISALLOWED OPTIONS: -e, -u
   IRRELEVANT OPTIONS: -a, -r

通過mode1產生的一個字尾為_dd.txt的檔案是degradome density file

第一次執行mode1；當降解組檔案不變，miRNA檔案改變時執行model2；當miRNA檔案不變，降解組檔案改變時執行model3；當兩個都存在時，執行model4（比如前面忘記作圖等等）
下面兩個常用的選項
-t 輸入結果為tabular format
-o 輸出降解組圖片