Comparing RNA levels in tumor/normal samples using RNA-seq

[Paul_N_Hengen]

Hi,

I'm starting a new cancer gene expression project using Illumina
RNA-seq fastq files for matched tumor/normal samples.

The experiment is geared toward comparing the RNA levels to see
if there is expression of some particular genes within the cancer
samples.

I have a few questions:

How do I determine if there are adapter sequences within the reads?
Will I need to trim these out?
What is the best way to remove them?

For efficiency, I plan to map the reads to only the particular genes
of interest as the reference genome and not map all reads to the
entire human genome/transcriptome using STAR aligner.

Do I need to include a few house-keeping genes in the mapping part
for normalization between tumor and normal and/or for normalization
across all tumor samples?

Are there any concerns about using the STAR aligner?

What is the best software tool to use for comparing the various gene
expression levels across all the samples?

Thanks in advance for any advice.