Part I: Library QC

I.I Library removed RNA due to duplicated or substring of other RNAs

We have 2679 sh/sgRNAs targeting 455 genes.

TargetMouse.sg1586 GCAGTCAAAACTCGAACAA Arpc5 19 Substring
TargetMouse.sg1995 GTGCAGAACGTTAGCTGAA Mapk1 19 Substring
TargetMouse.sg2631 TTGCTGAGGTTGCGCTTGC Gtf2a1 19 Substring

I.II Distribution of number of RNA targeting per gene

## [1] "Shuffle n.RNA cutoff is  6"

Part II: Mapping QC

II.I Mapping percentage and Coverage.

We have 6 samples.

sample n.matched total mapping.perc coverage.seq
1382255_F171_S3_L003_R1_001 15399918 17035686 90.39799 5748
1382256_F172_S4_L003_R1_001 18005292 20426396 88.14718 6721
1382257_F173_S5_L003_R1_001 18612129 20730694 89.78054 6947
1382258_F174_S6_L003_R1_001 8652723 11963920 72.32348 3230
1382259_F175_S7_L003_R1_001 18081107 20140061 89.77682 6749
1382260_F176_S8_L003_R1_001 17024698 19301564 88.20372 6355

II.II Log2 transformed raw count number distribution across all samples.

II.III Number of reads with n.mismatch percentage in each sample.

II.IV N.mismatch threshold QC.

## [1] "Suggested n.mismatch to rescue the most reads is  9"