Hi, I am (very) new at bioinformatics and I am currently dealing with getting appropriate genome and the annotations that goes with it in order to map RNA-seq data.
I am trying to get the appropriate annotations for the rhesus macaque genome. A recent assembly (rheMac8) is available on UCSC. However I cannot find any annotation for this genome on ensembl.
The 3 last releases of this macaque genome are rhemac2 (2005), rheMac3 (2006) and rheMac8 (2015).
The last annotation provided by ensembl is for rheMac2, so it seems that no annotation has been provided since, even if two new genome assembly have been released?
I also checked iGenome, in which the annotation provided is the one of ensembl, and I don't find anything on UCSC. I found an annotation on NCBI, but I have been advised not to use it as they are not really trustable.
I liftOver the annotation of rheMac2 on rheMac8 with STAR, but a lot of features end up in the failed liftover file.
I don't know how to deal with this, the rhesus macaque is the widely used as a monkey models, I don't understand why there is no appropriate annotation and what annotation thus people use.
Thank you! Camille
You might contact the Ensembl helpdesk and ask if they plan on including the most recent macaque genome in release 85.
Have replied to Camille but there may be other people interested in the newer assembly and annotation of Rhesus here too. Yes, it will be in Ensembl soon but not in release 85. Keep an eye on our blog and twitter account for news on this later this year.
Indeed, I contacted them and they said not in the release 85. Thank you!
In additional question related to this then, since I am comparing RNA-seq data from Macaque and Human, is it not a problem to use hg38 which is recent and well annotated, and compare it with data that I will map on a much older genome, with an old annotation? I'm worried that the differences I might find would be biased by the much better data available for human than macaque.
Cross-species comparisons are fraught with difficulties. What exactly are the comparisons you're hoping to make?
I have RNA-seq data coming from iPScells of Human and Macaque for several differentiation time points. We are interested in transposable elements (LTR7s).
I first want to check if these elements are expressed, then look if they are differentially expressed in the two species, and finally to see if those inserted in regulatory regions are more differentially expressed than the other. The purpose is to have a look at the role of the LTR in developmental differences between these two model species. (For the repeated sequence issues, I will use TEtranscript, a special pipeline that handle analysis of repeated sequence).
In this case yes, the completeness of the genomes is going to play a big role.