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Custom Genome Builder ๐Ÿ› ๏ธ ๐Ÿงฌ

Emily Georgiades, Hughes Group (September 2021)

Scripts to build a custom genome in order to align sequencing reads from edited cell lines.

This is a modified version of Caz's existing script, which can be found here:

<internal/path>

Required files:

  1. edited_region.fa
    This contains the sequence (no headers!) to be inserted between homology arms.

  2. genome.fa
    Use a symbolic link i.e.
    $ ln -s /path/to/file genome.fa

  3. genome.fa.fai
    Use a symbolic link i.e.
    $ ln -s /path/to/file genome.fa

  4. allTheOtherChromosomes.bed
    Coordinates for all other chromosomes. Download chrom.sizes from UCSC, remember to delete the chromosome that you're editing:

    $ wget https://hgdownload.cse.ucsc.edu/goldenpath/mm39/bigZips/mm39.chrom.sizes 
    $ awk -v OFS='\t' '{print $1, 0, $2}' mm39.chrom.sizes > allTheOtherChromosomes.bed
    
  5. chrX_split.txt
    Need to know coordinates of edited chromosome + deletion region.
    File should look like this (must be tab separated):

    chrX  0   xxxx  part_1  ## The chromosome up to deletion region
    chrX  xxxx  xxxx  part_2  ## WT region that is being swapped for the insert sequence. 
    chrX  xxxx  xxxx part_3  ## The remaining chromosome after deletion region.
    

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