I am interested in extracting sequence of a gene from a wild type and two allelic mutants of that gene. I have RNAseq data available from all three genotypes and i am wondering how do people normally go about doing this with RNAseq data ? One way i can think of is to denovo assemble the RNAseq reads from all three genotypes and pull out the gene sequence from all the three genotypes. Rather than doing this, Is there a way where you can extract the sequence from say BAM/SAM files?
Dear Upendra Kumar,
I would like to extract a gene sequence for 30 viral samples and planning to build a phylogenetic tree. For example, this is reference gene of interest for me NC_026434 which is NA Neuraminidase. For this gene, the CDS starts at1 and ends at 1410. How do I extract the same gene for all the 30 viral samples. I have the fastq files and reference aligned bam files.