Use one few genes instead of reference genome in mapping

Question

[bcube]

Hi.

My aim is to generate a phylogenetic tree from my analysis.

For this, I have a reference genome and Illumina reads of multiple samples.

I was thinking of using my own gene list generated from sequences downloaded from NCBI instead of using a reference genome for mapping.

Is this approach correct or do you guys have a simpler way?

Any suggestion will be much appreciated.

Thank you.

Answer 1

[lieven.sterck]

That is in essence not a bad approach, though it will also be sub-optimal (to some extent). The issue here being that when you only use a subsample to map your reads on you will never be sure perhaps some of the reads that align to your subsample would not have had a better (== true ) match against the rest of the genome/transcriptome. In theory you will have the same bias for all your samples so that might even it out a bit, but not eliminate it.

Bottom line: there is a risk to over-count the number of reads that map

[bcube]

Understood. Will use a reference genome. Thanks.

Answer 2

[swbarnes2]

Mapping to a truncated reference runs the risk of forcing reads to align where they do not belong. Don't do this. Align to a proper reference that contains all of the expected sequence.

[bcube]

Thank you very much. I will use the reference genome for mapping.