Bacterial RNA-seq analysis

Question

[mcff23]

Hi everyone,

I'm trying to analyze bacterial RNA-seq data and I want to know which pipeline is the best. I have a genome reference and it is annotated. Can I use Trinity to perform the analysis? Cufflinks?

Any hint on this would be great.

Thanks in advance!

Monica

[GouthamAtla]

It depends on what analysis do you want to perform. Btw, there should be tons of posts related to your question.

[mcff23]

I want to perform differential expression analysis. I just want to know which is the best pipeline to use in bacterial samples. For example I know that I can use bowtie2 or BWA to align my reads against the reference instead of using Tophat because I am working with bacteria. Do I have to consider others aspects in order to proceed with the analysis?

Thanks!

Answer 1

[Asaf]

I think that the best option is Rockhopper. It works well and it's fully automated.

[bandanaschapagain]

I am using Rockhopper for the bacterial RNA se datas. I gave the two .fastq files as input along with the reference. The two files are from two different experimental conditions. For differential gene expression I am getting 0% which is not helpful at all. Is there anything I am missing here? Thank

[Asaf]

Do you have one replicate of each condition? In that case I don't think Rockhopper can find differential genes

[bandanaschapagain]

I have two replicate for each condition. I really need help to figure it out this one. Best,

[Asaf]

You woke-up an old discussion, I think it would be better to open a new post describing your experiment and obstacles.