fulllength: Extract the full length transcripts sequences
In ZhenWei10/rBS2ndStructure: Filter the thermal stable RNA secondary structure

Description Usage Arguments Value See Also Examples

tx_seq_extraction is used to extract the fasta files of the full length transcripts.

tx_seq_extraction(BS_genome, TXDB, Write_PATH = ".",
  small_threashold = 4500, middle_threashold = 8000, trim_wsize = 2000,
  trim_ssize = 1000, divide_num = 30)

newf(x)

`BS_genome`	the `BSgenome` object of your organism.
`TXDB`	the `txdb` object of your organism.
`Write_PATH`	the path to write the transcript sequences.
`small_threashold`	the transcript length threshold to put into the small group.
`middle_threashold`	the transcript length threshold to put into the middle group.
`trim_wsize`	the window size for the trimming. By default, only the transcripts in the large group are trimmed.
`trim_ssize`	the step size for the trimming.
`divide_num`	the number of fasta files divided for each of the 3 groups. This argument is useful when conducting the parallel computation of the `RNAfold` step.

This function will create 3 folders named Small, Middle, and Big. Each of them will contains a number of fasta files containing the full length transcripts of the sizes of each group.

The number of the fasta files is determined by the argument divide_num.

RNAfold, Single_RNAfold, and rfold_assembly_tx

## Not run: 
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
tx_seq_extraction(MMusculus,txdb,getwd())

## End(Not run)