Would it be possible to align a whole RNA-seq against just a particular small set of transcripts, and not to a whole transcriptome? I.e., for example, just Hox genes, or just Wnt genes.
I am asking this because I am working with non-model organisms, with no genome or decent transcriptome available. After doing several attempts for a de novo assmebly transcriptomes, there was no way to get complete genes for most of those I am interested in, and way too many chimeric genes. But, after manually curating and tons of PCR I have now very reliable sequences for my set of transcripts. I would like to get expression level measures of this set of 43 genes in 8 developmental stages, and so although qPCRs are possible, I would rather try first to use the RNA-seq I have.
I thought on doing something similar to this: Create GFF from de novo assembly to input on htseq-counts
Align the RNA-seq datasets against the 43 genes (really low % of alignment expected), count the tags and calculate TPM myself. I just need the TPMs to then standardize (z-score) the data by gene.
Would that make sense?
Edit: edited title. I want to align and count