Best mapping tool for bacterial RNA (paired end sequence)

Question

[priya.saxena]

Hello Everyone,

I am trying to analyze rna-seq (paired-end) data generated from illumina, can anyone suggest me which tool for mapping will be best for it, I tried Bowtie-2 but unable to compare the results as I have 3 conditions and three replicates of each sample.

Thank You

[GenoMax]

I tried Bowtie-2 but unable to compare the results as I have 3 conditions and three replicates of each sample.

What does that mean? An aligner does not do the comparisons. You will use a program like DESeq2 or edgeR to do the actual statistical comparisons.

You have bacterial RNAseq, which is as simple an analysis as it can get. No splicing to worry about you can pretty much use any aligner for this task.

[priya.saxena]

Thank You so much.

can we compare 3 conditions at a time ? I am getting option for comparing two condition at a single time.

[ATpoint]

Please define what you mean by compare? Do you want to assemble transcriptomes, or make statements about differential genes, or something completely else, it is currently unclear what you aim to do.

[priya.saxena]

By compare I meant I have 3 samples and one of them is control, I need to compare the differential genes expression in both the samples with respect to my control. Moreover for each sample I have three replicates which I need to normalize.

[priya.saxena]

Thank you so much. I am extremely sorry for so much trouble. I am new to this field and trying to learn. Thank you so much for your guidance I really appreciate .