Can I directly map reads directly to genes instead of transcripts to estimate the expression in gene level?

[kerenzhou062]

Hi Josie,

I'm wondering that whether I can obtain the reads counts for gene by directly mapping reads to sequence from the whole gene locus instead of transcripts (minimap2 -ax splice)? Here is the example for the fasta file:

>ENSG00000240409.1 ATGCCCCAACTAAATACTACCGTATGACCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAATACAAATTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAAAAACTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCACTTCATTCATTGCCCCCACAATCCTAG >ENSG00000248527.1 ATGAACGAAAATCTGTTCACTTCATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATTACCACCCAACAATGACTAATCCAACTAACCTCAAAACAAATGATAGCCATACACAACACTAAGGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCTATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTGGAAGCGCCACACTAGCAATATCAACTATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTTACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAA >ENSG00000198744.5 ATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGGCCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCACAACCCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAGAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCTCCCACCCCCCAACTAGGGGGACACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGGGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTC

Thanks! Keren