Human Macrophage Transcriptome

Question

[gfwatson]

I have a set of reads that may be 80% human macrophage as determined by mapping and 20% parasite. To remove the reads I am not interested in, I would like to download a human macrophage transcriptome. I'm curious if there is a way to download the specific macrophage transcriptome or if I need to download the whole human transcriptome.

Answer 1

[Devon Ryan]

You don't specifically need to download a macrophage transcriptome, just align with STAR or a similar aligner to the human genome. The unaligned reads will be primarily parasite (with a couple random human reads that couldn't be aligned).