question of use AA for other species ref

[fanch1122]

I am a novice in the use of AA software. I see that the -ref option in the guide includes reference genomes for humans and mice, so I would like to ask if I can use other reference genomes to detect eccDNA of other species using WGS data through AA

[jluebeck]

Hi, at this time only hg19, GRCh37, GRCh38, and mm10 are supported. Providing additional support for references of other species requires the construction of an annotation database. Unfortunately that process is quite complicated and requires multiple different annotation files to be available from the UCSC genome browser and other sites. Not all species are as well-annotated as human and mouse so it may not be feasible for most species.

Thanks,
Jens

[fanch1122]

In fact, I want to use AA to find eccDNA from WGS data of other species
, I am thinking that this also requires very complicated annotations like you said, is there a relatively simple or easy way to implement it?

[jluebeck]

Which species do you have in mind? As mentioned above, the process is complicated and involves annotations from many sources. There is not a relatively simple way to do it.

[fanch1122]

I am currently working on paramecium related

[fanch1122]

I see AA's use method on the required data for WGS sequencing fastq files and genome fasta sequences for that species, is that true? If I don't need to annotate eccDNA specifically, can I use AA to do it?

[jluebeck]

The AA genome annotations are used for marking low complexity, repetitive regions, low-mappability regions, oncogenes, as well as areas that show high signal across many "normal" samples.

You would need to collect or generate analogous files for what is listed in the AA data repo. You will encounter many errors if you try to leave these kinds of files out of the analysis.

Thanks,
Jens