Alignment in bioinformatics

Question

[Monia]

my project talk about gene expression profile of Mycobacterium tuberculosis on lung , i choose my samples from ENA :https://www.ebi.ac.uk/ena/browser/view/PRJEB19976 , I download reference genome from NCBI : https://www.ncbi.nlm.nih.gov/genome/?term=h37rvand , I create an index by myself using HISAT2 and after that i started the process of alignmengt using HISAT2 either,now that's my score , i think it's pretty not good enough , but i don't know where is the problem , scores is not efficient , am i right ? is there any solution like changing the samples or any other ?

Answer 1

[ATpoint]

I see 90% alignment rate. That's fine probably. Cannot comment more only with the given information. Please do not ask for immediate help due to urgency, we're a community driven by volunteers. If people feel like answering they will.

Anyway, this is only one sample. What are you going to do with it?

[Monia]

Thank u for helping me ✨👋