Custom Genome Builder 🛠️ 🧬

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:

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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.