Mapping MISeq reads to a single gene
I am really new to genome analyses and i would like to use the community’s wisdom!
I have two simple tasks. Map MiSeq reads and call SNPs on 1)DNA and 2)RNA. Let me elaborate:
1) I want to simply identify SNPs between mothers and daughters on one specific amplicon. I think I should just simply map the reads to that amplicon using sth like Bowtie2 and then call SNPs with Samtools? Any better alternatives recommended?
2) I want to do sth similar, but in order to check if only a C to T SNP exists in RNA-seq data. The position of that SNP is known and the rest of the sequence should be the same. Can I use the same tools as in 1?
Thank you in advance!
Edit: The MiSeq reads are generated from only a region of a single gene. So it is not WGS, but only amplification of a targeted fragment.
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