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laurahspencer / DuMOAR

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Try mapping RNASeq R1 and R2 each alone #42

Closed laurahspencer closed 10 months ago

laurahspencer commented 11 months ago

using STAR to Dungeness genome with GenSas annotaiton

@ggoetznoaa trying this to see if it improves RNASeq alignment rates

laurahspencer commented 10 months ago

Unique mapping results using just R1, just R2, and paired. Full results in spreadsheet under tab "STAR R1/R2 GENSAS": https://docs.google.com/spreadsheets/d/16m-eGXqCJyl7LET2-P1hx4A5UW2YJeaK1UbswEqL1ls/edit#gid=469971862

Sample | R1-UniqueMapping | R2-UniqueMapping | Paired-UniqueMapping -- | -- | -- | -- CH01-06 | 27.57 | 27.67 | 25.38 CH01-14 | 34.89 | 34.83 | 32.41 CH01-22 | 30.71 | 30.76 | 28.14 CH01-38 | 25.9 | 25.93 | 24.06 CH03-04 | 26.92 | 27 | 24.58 CH03-15 | 18.7 | 18.78 | 17.55 CH03-33 | 29.28 | 29.66 | 27.52 CH05-01 | 25.04 | 24.99 | 23.17 CH05-06 | 23.68 | 23.7 | 21.78 CH05-07 | 39.96 | 39.87 | 35.98 CH05-09 | 26.33 | 26.41 | 24.63 CH05-14 | 31.64 | 31.65 | 29.59 CH05-21 | 14.8 | 14.87 | 14.11 CH05-29 | 31.38 | 31.41 | 28.19 CH07-04 | 45.77 | 45.53 | 40.8 CH07-06 | 34.74 | 35.25 | 32.21 CH07-08 | 25.2 | 25.41 | 23.94 CH07-11 | 32.95 | 33.23 | 30.48 CH07-24 | 28.1 | 28.26 | 26.34 CH09-02 | 20.07 | 20.02 | 18.72 CH09-13 | 19.47 | 19.48 | 17.62 CH09-28 | 40 | 40.38 | 37.01 CH10-08 | 26.08 | 26.08 | 24.44 CH10-11 | 26.81 | 26.79 | 24.58