TRUFA (Transcriptomes User-Friendly Analysis) is a free webserver designed to help you perform RNA-seq analysis.

So far, TRUFA is allowing you to execute the following steps (programs used are specified in the parentheses):

Reads cleaning:
Reads quality control (FASTQC)
Quality trimming...

READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples. Meanwhile is has been extended to process data generated in different...

Basic workflow for ChIP-seq analysis using Bioconductor from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389943/

Topic: ChIP-seq