Silene_RNASeq

Scripts for 2022 RNA Seq Paper (Silene)

1. Cleaning reads: SR_1_CleanReads.pl, sub_SR_1_CleanReads.sh
2. Transcriptome asssembly: SR_2_TrinityAssembly.sh
3. Find longest ORFs: SR_3_TransDecoder.sh
4. Quantify reads using kallisto: SR_4_KallistoQuant.sh
5. Analysis in R: DESEq2_script_formal_v13.R
6. Genomic regions without overlapping transcripts: SR_30.1_siteswithnooverlap.sh
7. GO enrichment: SR_31_GOenrichment.sh, SR_32_GOTerms.sh
8. Construct phylogeny: SR_33_hisat2.sh, SR_34_MergeBams.sh, SR_35_Genotype.sh, SR_36_MergeFilterSNPs.sh, SR_37_SNphylo.sh, SR_38_PlotTree.R