SSRs_and_TFs_identification.md

1. SSRs(Single sequence repeats) identification

a. Use MISA to find SSRs with default settings

 perl misa.pl ~/Phragmites_RNA/all_assemlies/renamed_for_abundance/cdhit_mrna_renamed.fa

b. Find the CDS-SSRs by comparing the SSRs list with tissue-specific DETs lists and coding region file

2. TFs(Transcription factors) identification

a. By comparing the TFs list of Setaria italica from PlantTFDB v5.0 with the annotation result from the alignment between the predicted peptide sequence file and S. italica annotated protein file via blastp.

b. Screen TFs with tissue-specific expression patterns, based on the lists of tissue-specific DETs from the previous step.