createProDB4DenovoRNASeq {PGA} | R Documentation

## Create protein database based on the transcripts from de novo reconstruction of transcriptome from RNA-seq data

### Description

Create protein database based on the transcripts from de novo reconstruction of transcriptome from RNA-seq data.

### Usage

    createProDB4DenovoRNASeq(infa = "./trinity.fasta", bool_use_3frame = FALSE,
      outmtab = "novel_transcripts_ntx.tab",
      outfa = "./novel_transcripts_ntx.fasta", bool_get_longest = TRUE,
      make_decoy = TRUE, decoy_tag = "#REV#", outfile_name = "test")

### Arguments

`infa` | A FASTA format file containing transcript sequences (such as derived from de novo transcriptome assembly by Trinity)
`bool_use_3frame` | A logical variable indicating whether to translate the raw sequences with 3-frame (forward). Default is 6-frame translation (FALSE).
`outmtab` | A txt format file containing the novel transcripts information
`outfa` | The output fasta format protein sequence file
`bool_get_longest` | When it's set as TRUE, only the longest protein sequences will be retained after the raw sequences are translated with 3-frame or 6-frame. Otherwise, all the protein sequences with longer than 30 aa will be retained.
`make_decoy` | A logical variable indicating whether to add the decoy sequences.
`decoy_tag` | The prefix of decoy sequence IDs.
`outfile_name` | Output file name

### Value

The database file(s)

### Examples

    transcript_seq_file <- system.file("extdata/input", "Trinity.fasta",package="PGA")
    createProDB4DenovoRNASeq(infa=transcript_seq_file)

[Package PGA version 1.8.1 Index]