Total gene discovered/detected is less than gene in reference genome

[pandapiggie]

Dear All,

I did a RNA-seq on my bacteria (Salmonella) samples for a differential expression study. I used the cufflinks pipeline for this study.

When I checked the results of cuffdiff it showed 3752 genes but when I checked the Salmonella reference gene list it shows a total of 4949 genes. How is there such a massive difference in the gene numbers?

As I understand some of the genes may not be detected due to inactivation or are hypothetical genes. However this is a not satisfactory answer for me and I would like to know if anyone has an explanation for this. I may be looking at the wrong keywords so if possible can someone please point me in the correct direction for me to read up on this?

Thank you.

[tristan dubos]

Hi,
I think it's a good result ! I'm not specialist in bacteria but if i remember rigth there is a big diversity in population and the genomic dynamic is intensive ( i speak about bacteria in general i don t know if this rules match for Salmonella). But if I’m right if you add the genomic diversity and the temporal expression plus extraction bias, at the end you have 75% of the genes describes , is not bad , don't you think ?
Depends at the end what are you looking for ?
An other point is i don't know witch databases you use but you have to be care about it because you have 2 types of information :
-Gene describe (protein expressed function etc )
-Gene predicted , based on functional domain who are described on other protein and genomic structure/pattern

[pandapiggie]

Hi Tristan,

Thanks for the input. I totally did not take into consideration the RNA extraction bias and the sequencing bias as well.

Thanks for your help.

I was using the RefSeq complete genome reference from NCBI as my reference.