I am starting to work with metatranscriptomics data and I don't know where to turn. A short recap:
I have 3 annotated bacterial genomes. I have 6 metatranscriptomes I have to map against them.
What I aim to: 1) know the expression of each genes in each genome; 2) compare the expression of genes between genomes (differential expression).
I already launched kallisto and got the abundance.tsv table. From here I don't know how to proceed and what tools to use. I have been suggest to divide the TPM by the mean length or the median length to obtain expression level within one genome, so that expression will be normalized both for length of transcripts and number of transcripts; and to use ALDEx2 or EDGE for differential expression analysis.
Also, where is best to handle data? Excel, R, Python?
I did some research on step by step tutorials and I couldn't find any recent one. Thanks for help!