Tutorials

Here is a list of some tutorials for GenomKit in handling various bioinformatic tasks.

Note

These tutorials are still under active development.

• Starting a FASTQ file
  • Trimming a FASTQ file for both sequences and quality
• Starting with a BED file
  • Get the sequences in FASTA format from a BED file
  • Get TSSs (Transcription Start Sites) and TTSs (Transcription Termination Sites) of genes in a BED file
  • Merging the nearby peaks in a BED file
  • Sampling the regions randomly in a BED file
  • Find the peaks in one BED file close to the regions in another BED file
  • Generate a heapmap from two BED files: one BED file is used as windows and the other used as the signal
• Starting with many BED files
  • Test the relevance of multiple peaks in BED files to different biotypes in GTF
• Starting with a GTF file
  • Get all the genes from a GTF file
  • Extract exon, intron, and intergenetic regions in BED format from a GTF file
  • Get all promoter regions in BED format from a GTF file
  • Extract the genes by their biotypes from a GTF file