Git repository for this sub-project: https://bitbucket.org/hotpollen/splicing-analysis/src/master/

Use gene mapping table to add gene descriptions to new annotations bed-detail file for SL5.0 genome assembly release and annotations.

Specifically:

• Get the BED-detail gene model file from IGBQuickload repository: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Jun_2022/S_lycopersicum_Jun_2022.bed.gz

The 13th column of this file contains a gene identifier. The 4th column contains a transcript identifier. The final (14th) column contains "NA" for "Not Available." We would like it to instead contain a description of the gene. Since we don't have that, we would like to insert the description of gene counterparts present in the SL4.0 annotations.

• Note that the SL4 annotations can be found here: http://lorainelab-quickload.scidas.org/quickload/S_lycopersicum_Sep_2019/S_lycopersicum_Sep_2019.bed.gz

To map genes from SL4 onto SL5, you need a mapping file. The people who made SL5.0 gave us that mapping file back in July 2022:

Dear Ann,
Yes, we do have tables for the conversion between different versions. They are now avaiable on our website (http://solomics.agis.org.cn/tomato/ftp/ID_convert/).
Thanks so much for the intergration! I would be happy to forward it to my colleagues when it is avaiable.
Best regards,
Yao

Mapping files needed are also available in: /nobackup/tomato_genome/alt_splicing/mappingfiles