Hi friends,

I am going to 8 bacterial bulk RNAseq samples. I am interested in doing following bioinformatics analyses for the 12 samples.

a) Trimming of the reads

b) Alignment of the RNA-seq reads to the reference bacterial genome

c) ID and construction of splice-junctions

d) Reports of known transcripts with annotation and abundance

e) Report of novel transcripts and abundance

f) Testing differential expression

g) GO and Kegg annotation and enrichment analysis

h) Also, DeNovo Assembly 


**1) For mammalian, I used the following softwares Tophat, cufflinks, cuffmerge, cuffquant, and cuffdiff? 
2) Is there any separate tools/pipelines for bacterial RNAseq data?
3) What are tools for GO, Kegg and enrichment analysis?
4) Which denovo assembly tool is recommended for bacteria?**


For # 1 since you would not expect splicing to be an issue you could use any aligner (I recommend BBMap suite for trimming/alignment).<br> #2 there are dedicated pipelines available for bacterial RNAseq. [Rockhopper][1] is a web based one. Search Entrez for others. <br>#3 You should be able to use GeneSCF (https://www.biostars.org/p/108669/ ). <br>#4 [SPAdes][2] is about the best bacterial genome assembler.


  [1]: https://cs.wellesley.edu/~btjaden/Rockhopper/
  [2]: http://bioinf.spbau.ru/en/spades