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commands for RNAseq data analysis and variation(snp)

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

rna-seq
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written by miravet65 • miravet65

And this one for variant calling.

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written by h.mon h.mon

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