7.7 years ago by
This will depend on whether your macrophage's genome is "known" or not. Do note that "known" is always a quite relative thing, but here I mean that there is a correctly annotated genome available.
If this is the case, it should be fairly easy:
- get the transcriptome data from the genome using its annotations.
- map your RNA-seq reads to the macrophage transcriptome (using a mapping tool like SOAP or BWA)
- remove all reads mapping to the macrophage transcriptome
If your macrophage's genome is not "known", is there a large amount of data on it that is available, or from a very closely related species? If so, you should adapt the above procedure (namely lowering mapping thresholds) to remove all reads mapping to the sequence information you have. If not, you are in front of an open problem in bioinformatics, congratulations :-) If you are willing to share some more details on your project, we might then still be able to help by providing some ideas on how to proceed.