Hi, I have human rna-seq data and I'm using htseq-count to get the number of reads that map to Ensembl genes. I believe htseq-count uses a union model to summarize the transcripts into genes. How can I get the either the coordinates of the gene model and/or the length? After htseq-count, I would like to use UPC software (http://jlab.bu.edu/software/scan-upc/) which requires as input the number of reads mapping to each gene, the length of the gene, and the GC content of the gene.
Thank you for your input.
Thank you for your input.