OutputJunctions: Output Splice Junction FASTA
In mffrank/RNAseqToCustomFASTA: Produce Custom Protein Fasta Databases from RNAseq Data

Takes STAR output files (SJ.out.tab as input and outputs a named numeric vector (names = Transcript/gene id, value = FPKM)

1 2	OutputJunctions(outfile, juncs, exons, procodingseq, proteinseq, genome, alt_spl = TRUE, all_junc_peptides = TRUE, trimTry = TRUE)

`exons`	Exon table from annotation folder
`procodingseq`	Protein coding sequences from annotation folder
`jun`	Junction file produced by the JunctionType function

mffrank/RNAseqToCustomFASTA documentation built on May 22, 2019, 7:55 p.m.

mffrank/RNAseqToCustomFASTA index

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