Mapping MISeq reads to a single gene

Question

[panosprov]

Hello community,

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.

[Pierre Lindenbaum]

. I think I should just simply map the reads to that amplicon

no, use the whole genome. Mapping whole exome sequencing

[panosprov]

Why? To make sure we have not amplified other genomic sequences? What about the mapping and SNP calling tools to use?

Maybe it was not clear in my original post, but we have used primers to amplify only a sequence of one gene prior to using MiSeq.

[Pierre Lindenbaum]

Why ?

see Wouter's answer:

You will create false positives and false negatives by preselecting regions.