Compute the cross mappability for rat genome

1. Reference genome versions and other details can be found in RatGTExPortal.
   1. Libraries were sequenced using 150-bp paired-end sequencing.
2. Cross-mappability calculated based on original for human, modified for rat

Preparation of files

1. Run gem_index.sh to index genome, take about 1 hour to index whole rat genome.

• Need to make a copy of reference genome that splitted by chromosome for downstream analysis.
• Using 12G memory.
• The BigWig output contains a column with dna, need to remove this column for downstream process.
• The paper tested different lengths of k-mer but didn't provide any details about how to choose k-mer. Based on the descrition, they use the read length as the length for exon. So we are going to use the same setting here.

2. Potential issues:

• The paper build index using Bowtie which may not aware of the splicing event.

3. Download bowtie 1.2.2 and index genemo using command bowtiew-build <ref_genome> <prefix>.

• Bowtie does not work on Expanse, not sure why. Built the index on snorlax.

Compute Cross-mappability

1. Modules need to be load :

• R: r/4.0.2-openblas, cpu/0.15.4 gcc/9.2.0
• Modifications to the cross_mappability repository:
  1. For all Rscript, need the change the argpharser - to --
  2. Need to install library, using env.R files. Add library path to all scripts.
  3. In the compute_mappability.R and gtf_to_bed.R, need to change the code to get the utr in rat gtf which specified as 'three_prime_utr', 'five_prime_utr'.
  4. In the compute_mappability.R, the rat ref genome contains more contigs, some contigs only exist in exon, need to change the code avoid error message.
• Export bowtie path

2. To run jobs:

• Haven't optimized the workflow, just used the original one. There are different part in set_variables.sh, run each single part sequentially by comment off other parts. Maybe use snakemake to better organize the workflow.
• Set user_slurm=0, Run bash set_variables.sh in an interactive node
• Set user_slurm=1, Run bash set_variables.sh <expans_account> to submit jobs