Question: Bacterial RNA-seq analysis
0
gravatar for mcff23
3.2 years ago by
mcff2360
mcff2360 wrote:

Hi everyone,

I'm trying to analize 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 • 2.9k views
ADD COMMENTlink modified 3.2 years ago by Asaf5.3k • written 3.2 years ago by mcff2360

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

ADD REPLYlink written 3.2 years ago by geek_y9.3k

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!

ADD REPLYlink written 3.2 years ago by mcff2360
3
gravatar for Asaf
3.2 years ago by
Asaf5.3k
Israel
Asaf5.3k wrote:

I think that the best option is Rockhopper http://cs.wellesley.edu/~btjaden/Rockhopper/ . It works well and it's fully automated.

ADD COMMENTlink written 3.2 years ago by Asaf5.3k

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

ADD REPLYlink written 18 months ago by bandanaschapagain30

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

ADD REPLYlink written 18 months ago by Asaf5.3k

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

ADD REPLYlink written 17 months ago by bandanaschapagain30

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

ADD REPLYlink written 17 months ago by Asaf5.3k
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