genes_modified_THRA_isoforms_v2.gtf

We edited the genome reference (Gh38) to map exon 9b exclusively to THRA1 and exon 10 exclusively to THRA2. Exons 1 to exon 9a were set to map to THRA. To achieve this, entries corresponding to exon 10 (chr17:40,093,020-40,093,613 (+), chr17:40,093,137-40,093,867 (+) and chr17:40,093,020-40,093,867 (+)) were given a new gene_id, transcript_id and gene_name “THRA2” to make it count as a separate gene and allow mapping with Cellranger. Entries corresponding to exon 9b were given a new gene_id, transcript_id and gene_name “THRA1” and their starting position was edited to avoid overlapping with exon 9a mapping to THRA (chr17:40,089,334-40,092,627 (+) and chr17:40,089,334-40,089,730 (+)).

Please refer to the linked publication for more details on generation and usage