lzamparo / crisprml Goto Github PK
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License: BSD 3-Clause "New" or "Revised" License
Library design for CRISPr screen
License: BSD 3-Clause "New" or "Revised" License
We have 324561 exons split across 94838 transcripts.
We have 242027 unique exons to cover.
We have 1534276 guides that are specific enough for our purposes that cover those exons.
Now we have to choose a guide per exon to make up a feasibly sized library. There are far more guides than are required, and even then too many exons to cover even if we choose one guide / exon.
Will discuss with Turgut tomorrow, but for now I'll see how many exons we need to cover if we consider just the first two exons of each Tx.
Looks like this is a trivially parallel problem; each guide does not depend on the choices of any other guide, so I should be able to speed up the computation by data-parallelism across chromosomes
From the feature_generation_from_sequence.sh
script, two of the inputs common to each job are
mismatch="/cbio/cllab/home/aperez/Scripts/Project_Scripts/Ventura_CRISPR/active/crispr-project/guidescan-crispr/guidescan/CFD_scoring/mismatch_score.pkl"
pam="/cbio/cllab/home/aperez/Scripts/Project_Scripts/Ventura_CRISPR/active/crispr-project/guidescan-crispr/guidescan/CFD_scoring/pam_scores.pkl"
Need to recover these files, either from Alex' storage on Hal, or Yuri's backup on Lilac
Since I'll be running these on an LSF-based cluster, re-write scripts to conform to job submission standards
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