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Bacterial RNA-seq analysis

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

rna-seq bacteria
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updated by Ram Ram • written by mcff23 • mcff23

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

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written by GouthamAtla GouthamAtla

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!

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updated by Ram Ram • written by mcff23 • mcff23

1 answer

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

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updated by Ram Ram • written by Asaf Asaf

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

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written by bandanaschapagain • bandanaschapagain

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

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written by Asaf Asaf

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

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written by bandanaschapagain • bandanaschapagain

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

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written by Asaf Asaf

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