commands for RNAseq data analysis and variation(snp)

Question

[miravet65]

hi I want RNA-seq data analysis .I do not have enough information in commands and software.which soft ware must be use for analysis in each step. i want commands for linux and R program. can i replace my data in general commands linux for analysis?If you help me I would be thankful commands for 1 quality control 2 alignment 3 read count 4 normalize and expression

[cpad0112]

Please follow this tutorial : https://www.bioconductor.org/help/workflows/rnaseqGene/

[h.mon]

And this one for variant calling.