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>
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edited_region.fa
This contains the sequence (no headers!) to be inserted between homology arms. -
genome.fa
Use a symbolic link i.e.
$ ln -s /path/to/file genome.fa
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genome.fa.fai
Use a symbolic link i.e.
$ ln -s /path/to/file genome.fa
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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
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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.