Transdecoder预测转录本的开放阅读框（CDS）

首先trinity生成的fasta文件

安装Transdecoder（我是通过conda安装的，也可以去下载安装包自己解压加环境）

运行TransDecoder.LongOrfs

$TransDecoder.LongOrfs -t /data1/spider/ytbiosoft/data/trinity.all/trinity_out_dir_all.Trinity.fasta   

结果如下：

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(bioinforspace) [spider 04:01:18 e[35;1m]/data1/spider/ytbiosoft/data/trinity.all/TransDecoder.LongOrfs

$TransDecoder.LongOrfs -t /data1/spider/ytbiosoft/data/trinity.all/trinity_out_dir_all.Trinity.fasta

-- Skipping CMD: /data1/spider/miniconda3/envs/bioinforspace/opt/transdecoder/util/compute_base_probs.pl /data1/spider/ytbiosoft/data/trinity.all/trinity_out_dir_all.Trinity.fasta 0 > /data1/spider/ytbiosoft/data/trinity.all/TransDecoder.LongOrfs/trinity_out_dir_all.Trinity.fasta.transdecoder_dir/base_freqs.dat, checkpoint [/data1/spider/ytbiosoft/data/trinity.all/TransDecoder.LongOrfs/trinity_out_dir_all.Trinity.fasta.transdecoder_dir.__checkpoints_longorfs/base_freqs_file.ok] exists.

- extracting ORFs from transcripts.

-total transcripts to examine: 375779

[375700/375779] = 99.98% done    CMD: touch /data1/spider/ytbiosoft/data/trinity.all/TransDecoder.LongOrfs/trinity_out_dir_all.Trinity.fasta.transdecoder_dir.__checkpoints_longorfs/TD.longorfs.ok

#################################

### Done preparing long ORFs.  ###

##################################

    Use file: /data1/spider/ytbiosoft/data/trinity.all/TransDecoder.LongOrfs/trinity_out_dir_all.Trinity.fasta.transdecoder_dir/longest_orfs.pep  for Pfam and/or BlastP searches to enable homology-based coding region identification.

    Then, run TransDecoder.Predict for your final coding region predictions.

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运行TransDecoder.Predict

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$TransDecoder.Predict -t /data1/spider/ytbiosoft/data/trinity.all/trinity_out_dir_all.Trinity.fasta  结果如下：

-rw-rw-r-- 1 spider spider      1449 Apr 11 19:48 pipeliner.38661.cmds

-rw-rw-r-- 1 spider spider       296 Apr 11 20:01 pipeliner.38864.cmds

-rw-rw-r-- 1 spider spider      3644 Apr 11 20:41 pipeliner.40446.cmds

-rw-rw-r-- 1 spider spider      3350 Apr 11 20:38 pipeliner.41631.cmds

-rw-rw-r-- 1 spider spider  16515704 Apr 11 20:40 trinity_out_dir_all.Trinity.fasta.transdecoder.bed

-rw-rw-r-- 1 spider spider 104584265 Apr 11 20:43 trinity_out_dir_all.Trinity.fasta.transdecoder.cds

-rw-rw-r-- 1 spider spider  75371916 Apr 11 20:39 trinity_out_dir_all.Trinity.fasta.transdecoder.gff3

-rw-rw-r-- 1 spider spider  44730662 Apr 11 20:41 trinity_out_dir_all.Trinity.fasta.transdecoder.pep

drwxrwxr-x 3 spider spider      4096 Apr 11 20:38 trinity_out_dir_all.Trinity.fasta.transdecoder_dir

drwxrwxr-x 2 spider spider      4096 Apr 11 20:43 trinity_out_dir_all.Trinity.fasta.transdecoder_dir.__checkpoints

drwxrwxr-x 2 spider spider        52 Apr 11 20:12 trinity_out_dir_all.Trinity.fasta.transdecoder_dir.__checkpoints_longorfs

其中：

*.pep （是最终的候选ORF编码的蛋白序列）

*.cds （是编码蛋白的核酸序列）

*.gff3 （是表示ORF和转录本的位置关系）

*.bed （用于后期的IGV可视化）

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