TALON
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Problem with talon_initialize_database
Tried to run talon_initialize_database but got an error:
talon_initialize_database --f reference/GRCh38_GENCODE_rmsk_TE_reformatted.gtf \
--g hg38_rmsk_ucsd \
--a hg38 \
--o hg38
chrY
bulk update genes...
bulk update gene_annotations...
Traceback (most recent call last):
File "/home/kilian/anaconda3/envs/talon/bin/talon_initialize_database", line 8, in <module>
sys.exit(main())
File "/home/kilian/anaconda3/envs/talon/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 1073, in main
populate_db(db_name, annot_name, chrom_genes, chrom_transcripts, exons, genome_build)
File "/home/kilian/anaconda3/envs/talon/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 634, in populate_db
add_transcripts(c, transcripts, annot_name, gene_id_map, genome_build)
File "/home/kilian/anaconda3/envs/talon/lib/python3.7/site-packages/talon/initialize_talon_database.py", line 743, in add_transcripts
db_gene_id = gene_id_map[native_gene_id]
KeyError: 'AluY'