TODO_SGSeq_notes.md

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

• SGSeq: https://bioconductor.org/packages/3.16/bioc/vignettes/SGSeq/inst/doc/SGSeq.html

• plotCoverage() shows coverage by exon, and arcs per splice

• plotSpliceGraph() plots schematic splice graph, flattened per gene.

• TxFeatures class: importTranscripts() from GFF/GTF file, or GRangesList

• code converts TxDb using convertToTxFeatures()

• this function converts exons to GRanges
• it creates junction regions between exons, also GRanges
• exons have one or more txName, (CharacterList), and one or more geneName (CharacterList, maybe multiple are allowed?)

• exons have a type:

  • J (splice junction)
  • I (internal exon)
  • F (first/5'-terminal exon)
  • L (last/5'-terminal exon)
  • U (unspliced transcript).

• SGFeatures class:

• TxFeatures can be converted with convertToSGFeatures()

• model of disjoint exons spliced into transcripts

• exons have a type:

  • J (splice junction) - this junction could be used in splicejam
  • E (disjoint exon bin) - this exon could be used in splicejam
  • D (splice donor site) - this point feature is not used in splicejam
  • A (splice acceptor site) - this point feature is not used in splicejam

• featureID unique identifier

• txName CharacterList of transcripts; geneName CharacterList of genes

• Input typically by BAM file, STAR or GSNAP that custom tag XS for spliced reads

• si (sample information) is a data.frame with these columns:

  • sample_name: character unique sample label
  • file_bam: character BAM alignment file
  • paired_end: logical indicating whether reads were paired
  • read_length: integer length of each read
  • frag_length: integer fragment length
  • lib_size: integer total aligned fragments

• getBamInfo() can be used to create this data.frame:

  • path <- system.file("extdata", package = "SGSeq")
  • si$file_bam <- file.path(path, "bams", si$file_bam)

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.