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7.5 years ago
zh.khodadadi
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20
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
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
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.
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.
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
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to answer to earlier comments, as such this thread remains logically structured and easy to follow.ok thanks for this guidance