My data is got from 2 tissues by Illumina sequencing with 75nt reads. Are there any standard ways to study differential expression?
Is it necessary to calculate RPKM for each gene? If so what is the best tool to calculate RPKM? ERANGE, TopHat or Cufflinks?
Is simply counting and comparing the number of reads mapping to each gene between tissues also acceptable for studying differential gene expression?
Thank you for your time!
Is it necessary to calculate RPKM for each gene? If so what is the best tool to calculate RPKM? ERANGE, TopHat or Cufflinks?
Is simply counting and comparing the number of reads mapping to each gene between tissues also acceptable for studying differential gene expression?
Thank you for your time!
Comment