Looking for chimp genome index (STAR)

Question

[compuTE]

Hello,

Does anybody know where could I find a pre-made genome index for chimpanzee to run STAR Aligner? I need it to be pre-made, I know it is easy to do but I still need it pre-made.

I saw @Alex have some of them here but I couldn't find the chimpanzee.

Any help would be well appreciated.

[Bastien Hervé]

I don't think you'll find a pre-made index file for chimpazee easily over the web. May I ask you why you can't create the index yourself with the chimpanzee reference genome ? If you have memory issue with STAR I suggest you to switch to HISAT2 which is memory costless

[compuTE]

I want the support from the server I work at to add the genome index because I will be using it on the daily basis. But they are pretty picky on what they add to the server, so I was wondering if I could find something from the creator of STAR or some reliable source. But I guess as you said it is going to be hard to find, so I can offer them a good reference genome and that they can run it. Thank you anyway!

[igor]

It's hard to define a reliable source.

For example, the human genome is by far the best maintained and annotated. However, there are still many versions of the FASTA that are all the same build. This is a nice summary of the problem: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

Adding gene annotations (there are multiple different sources: Ensembl, NCBI, UCSC, GENCODE) on top of that yields even more combinations.

To summarize, there are a lot of decisions you have to make when selecting the correct reference. You may as well build the index yourself.

Answer 1

[igor]

Illumina attempted to compile a collection of reference sequences and annotation files for commonly analyzed organisms: https://support.illumina.com/sequencing/sequencing_software/igenome.html

They don't provide the STAR index, but they do provide the FASTA and the GTF files that the index is built from. However, for chimpanzee (Pan troglodytes), there are 7 different "official" versions, so you still have to decide which is the "right" one.

[compuTE]

Thank you so much! I will use this