PGA (version 1.2.2)

createProDB4DenovoRNASeq: 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)