Prokaryotic Differential expression analysis- RNA seq data and software
Hi every body I want to analyze(Differential expression ) my rna seq data of bacteria single end read,50 bp, Illumina HiSeq 2000. Can I use tuxedo software? What is the pipeline of Differential expression analysis for bacteria rna seq data? thanks a lot
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zh.khodadadi •
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Since you don't need to account for splicing you could use any NGS aligner and count the reads that are aligning to the genes using an annotation file (GTF/GFF). This can then be followed by one of the popular DE analysis programs DESeq2/edgeR etc.
An online pipeline is mentioned in this thread (if that is of interest): Bacterial RNA-seq analysis
Dear genomax2, Hi
Is this pipeline helpful for bacteria?
FastQC --> Trimmomatic/Cutadapt --> STAR --> Samtools --> featureCounts/HTseq-count --> DESeq2
STAR can output sorted bam, so I'm not sure why you add samtools in there ;)
Hi,
I have used it from other Biostars posts, so it should be :
FastQC --> Trimmomatic/Cutadapt --> STAR --> featureCounts/HTseq-count --> DESeq2
Seems valid, but as @genomax2 already wrote a spliced aligner isn't really necessary (because no splicing in bacteria), and I also would run fastQC after trimming to see how successful it was.
I am partial to BBMap suite so I would do
BBMap will output bam files directly (as long as samtools is available in $PATH, but you would need to sort them). featureCounts will sort BAM's automatically, in case you do not want to use samtools.
Dear zh.khodadadi, Hi
Do you have any reference genome for your bacteria of interest?
~ Best
thanks all I am new in NGS why I dont use Tuxedo pipeline?
My bacteria has reference genome and I study some posts like that genomax2 says.
Please use
ADD REPLYto answer to earlier comments, as such this thread remains logically structured and easy to follow.ok thanks for this guidance