I have 6 wheat samples sequenced using RNA-seq. I received forward and reverse fastq files and I generated bam files by using hisat2 tool which are aligned with the reference wheat genome. I have been asked to build multiple sequence alignment for 3 genes from this sequenced rna seq data. I believe I need to select a gene sequence from all the samples and do a multiple sequence alignment. But I am struck in fetching the gene sequence from bam files. How do I select one gene sequence for all the 6 samples? Any suggestions? kidly send me commands for fetching the sequence of genes from this RNA seq data in fastq file or aligned.bam file.