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Salmon to map ALL RNASeq reads to the trinity de-novo transcriptome built from MEGAN-scrubbed reads #43

Closed laurahspencer closed 10 months ago

laurahspencer commented 11 months ago

NEW APPROACH given that the de-novo transcriptome built from MEGAN-scrubbed reads might be pretty good, as per BUSCO results (~92% complete):

@ggoetznoaa use Salmon to map ALL RNASeq reads to the trinity de-novo transcriptome built from MEGAN-scrubbed reads.

laurahspencer commented 10 months ago

Complete! Results are here: https://github.com/laurahspencer/DuMOAR/tree/main/results/salmon/all.original_vs_megan6_assembly

See alignment rates by sample in the "Salmon Mapping" tab of this spreadsheet: https://docs.google.com/spreadsheets/d/16m-eGXqCJyl7LET2-P1hx4A5UW2YJeaK1UbswEqL1ls/edit#gid=1978455969

Script: https://github.com/laurahspencer/DuMOAR/blob/main/scripts/giles/run.salmon.align.all_original.megan6_trinity_assembly.sh