On the way to my own bioinformatics pipeline I found the following websites helpful.

General:

• What is RPKM, FPKM and TPM again? http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/

Alignment tools:

• TopHat2 and Bowtie version compatibility: https://github.com/fomightez/tophat_and_bowtie
• Example of Tuxido Suite workflow and differential gene expression analyis: https://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/user/523/documents/zebrafish-rna-seq.pdf