Documentation
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Overview ¶
This is the main package for parsegencode. It accepts a gencode GTF, a genome fasta and prints transcript fasta records to a user-specified (or default) outfile, optionally padding the exons by any number of bases.
To run parsegencode minimally:
parse_gencode /path/to/gencode_gtf /path/to/genome_fasta
This will create /path/to/genome_fasta_parsed.fa
To pad exons by 20bp parse_gencode /path/to/gencode_gtf /path/to/genome_fasta -exon_padding 20
See `func Usage` for more details.
Index ¶
Constants ¶
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Variables ¶
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Functions ¶
func DetectFusion ¶
DetectFusion is the main entry point for AF4 fusion detector.
func GenerateTranscriptome ¶
GenerateTranscriptome generates the AF4 transcriptome FASTA file from the given inputs. gtfPath is gencode comprehenve antotation file (e.g., gencode.v26.annotation.gtf), and fastaPath is the reference genome (e.g., hg38.fa). gtfPath may be compressed, but fastaPath must be uncompressed.
Types ¶
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Source Files