Hi, so i am pretty new to this whole computational process. I have no experience with any "R" packeges. I have only used commercial softwares.(CLC genomics workbench). It would be awsome if you guys can give me detailed suggestions and links so i can practice.
Before I begin let me describe my samples.
method: cDNA library 100bp paired-end -> illumina hiseq -> Raw data processed(TPM) with CLC genomics workbench
*GOAL: * I am trying to compare expression levels between samples Treated VS Not Treated (with replicates)
====================!!!!!So *here are the questions i have!!!!!*=================================
1.My treated sample had a small population when i isolated the total RNA for RNA-seq. I observed that the mapping % between Treated and Non-treated show a big difference(non treated control mapped around 17 times more compared to treated sample). Is there any way to normalize for this difference. It's not like i can just multiply 17 to the treated samples to make up for the low mapping %, right?
- When i normalize the raw data(Fastq), which normalization process must be considered? I have used TPM for transcript length and sequencing depth but I am new to this whole RNA-seq criteria and i need some serious help. any suggestions?
I dont have that much experience for computational processing. I would be greatful if you could give me detailed suggestions or methods.!!!!