add protocol for threedrnaseq

assays/Salmon_quantification/protocols/TranscriptQuantification.md

 ## Transcript Quantification with Salmon
 
-To quantify transcripts, all cleaned reads were mapped to the BaRT1 reference (Rapazote-Flores et al., 2019) using Salmon (v. 0.14.1) (Patro et al., 2017), and the mapping rates were estimated with an average of ∼93%. We kept transcripts with a minimum of 1 CPM (counts per million) in at least three samples. Normalization of TPM (transcript per million) was conducted using the ‘ThreeDRNAseq’ R package (v2.0.1) (Guo et al., 2021). For TPM values, see Supplementary Dataset 2 and 3. As the samples were collected at different DAEs and RNA extraction was conducted in several batches, we removed the batch effect in the gene count by using the ThreeDRNAseq’ R package (v2.0.1) (Guo et al., 2021).
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+To quantify transcripts, all cleaned reads were mapped to the BaRT1 reference (Rapazote-Flores et al., 2019) using Salmon (v. 0.14.1) (Patro et al., 2017), and the mapping rates were estimated with an average of ∼93%.
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assays/ThreeDRNAseq/protocols/NormalizationWithThreeDRNAseq.md

+## Normalization with ThreeDRNAseq R package
+
+We kept transcripts with a minimum of 1 CPM (counts per million) in at least three samples. Normalization of TPM (transcript per million) was conducted using the ‘ThreeDRNAseq’ R package (v2.0.1) (Guo et al., 2021). For TPM values, see Supplementary Dataset 2 and 3. As the samples were collected at different DAEs and RNA extraction was conducted in several batches, we removed the batch effect in the gene count by using the ThreeDRNAseq’ R package (v2.0.1) (Guo et al., 2021).
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