custom reference genome for RNA-seq

[enelkinsan]

Dear all,
I have RNA-seq data with 20 target genes and 5 reference genes (human). I don't want to map it to the whole genome because I'm only interested in those 25.
Probably, there is a way to modify (or build) an index for human so that it will include only 25 "chromosomes"? I'm just stuck in the middle of bowtie manual wandering where to look for the answer.

Thanks,
Elizabeth

[rflrob]

If you have a fasta file with those 25 genes, you can then run bowtie-build on that, and then use the resulting index for bowtie or tophat.

[Simon Anders]

How comes that your sample only contains data from these 25 genes? Have you used 25 primer pairs to pre-select for them? If so, why did you use RNA-Seq and not qPCR?

If you do an unusual kind of assay, please give details when asking for help here, or you waste everybodys time.

In case you meant that you have ordinary RNA-Seq samples from the whole polyadenylated RNA fraction but are only interested in these 25 genes: Then do an ordinary analysis and map to the whole genome as usual. Otherwise you risk mapping reads to your genes that were from different regions because the aligner could not see that the mapping is ambiguous because you hid the full genome from it.