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?
Hi, I just begin in the RNA seq analysis field and I am working with bacteria as well. Did you find the right pipeline? I am looking for the better tool for aligment step
Hey, how about starting with this guide: https://www.annualreviews.org/doi/abs/10.1146/annurev-biodatasci-072018-021255 Written by some of the more well-known names in the RNA-seq field. It contains alot of background any helpful suggestions. This workflow is also helpful. https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html The principles of RNA-seq are basically the same for bacteria just that you do not need to use a special software that is splice-aware for alignment or quantification.
Thanks Atpoint for the advices! Was really useful I´ve been reading and I found the SPARTA pipeline. I will try.