Running Mandalorion per chromosome

[abayega]

Hi,

I was having issues with the script 'Mandalorion_7_Gene_expression.py' ; it was hanging on the read_data function at a specific line and never moving on. I created a script that loops across all chromosomes and supplies all that is needed to run this script at a per-chromosome level. My question is, do I need to keep 'counter' constant (to the total number of lines in '2D_trimmed_l_gmapoutput_filtered_psl') to perform the normalisation on total number of mapped reads?

Thanks