Barley Phenology 2023

Data used in the analysis is located in the "data" folder. All relevant scripts, including python scripts and jupyter notebooks are in the "script" folder.

Blast result collecting and tpm data extraction

1. Blast GEMOMA result with GsRTD protein database

Protein sequences from GEMOMA result were BLAST against GsRTD protein database with corresponding variety using NCBI blastp

# Example Morex
blastp -db Morex.GsRTD.db -query Morex.gene.1.fa -out Morex.gene.1.txt -outfmt 6

2. Merge blast result

merge_blast_result.py

Reads the BLAST result from files and write them to a merge file

3. Match TPM by GeneID

match_tpm.py

Reads cleaned merged BLAST results from a table and match them with the TPM by geneIDs.