I have 2 RNA-seq files for two samples and aligned them to the reference genome so I have BAM files. I would like to get the read density of the first 1000 nucleotides for all transcripts and then get the average of that in such a way I would get one value per sample (which is average read density for the first 1000 nt of all transcripts) . so far, in python I have got a dictionary containing one transcript per gene as a representative of gene (in this dictionary I have the gene name and transcript name). do you guys know how I can get the read density of the first 1000 nt for each transcript? the I can get the average of that.