How to construct TE reference for other species?

[bio-xtt]

Hello, I want to build reference for species Chimpanzee, Macaca fascicularis and so on, scTE has built reference TE for these two species, I would like to ask how to build with MATES, is there a corresponding tutorial?

[Szym29]

Hello @bio-xtt ,

Thanks for your interest in using our tool. In the https://github.com/mcgilldinglab/MATES/tree/main/example, we mentioned that

If you have species other than human/mouse, downloaded TE reference in csv format and gene refrence in GTF format from UCSC table browser, run:

python build_reference.py Other path_to_TE_reference path_to_Gene_reference

## A sample of D.melanogaster TE refrence downloaded from UCSC table browser:
$ cat TE_reference.csv | head
#"bin","swScore","milliDiv","milliDel","milliIns","genoName","genoStart","genoEnd","genoLeft","strand","repName","repClass","repFamily","repStart","repEnd","repLeft","id"
"73","845","199","35","16","chr4","130778","131107","-1217024","-","DNAREP1_DM","RC","Helitron","-82","512","268","8"
"74","18658","190","35","41","chr4","1307882","1314210","-33921","-","HETA","LINE","Jockey","-1","6080","1","8"
"585","416","0","0","0","chr4","0","355","-1347776","+","(TTATTATA)n","Simple_repeat","Simple_repeat","1","355","0","8"
"585","15","134","29","29","chr4","688","723","-1347408","+","(TAA)n","Simple_repeat","Simple_repeat","1","35","0","8"

You can also follow UCSC table browser use guide to download TE and gene reference.

Thanks, Yumin

[bio-xtt]

Thank you very much. The following error occurred when I constructed human TE reference. How can I solve it?

[Szym29]

Hi @bio-xtt ,

I have fixed this issue and updated the code. Please git clone the code again.

Thanks for your interest. Please feel free to contact us if you have any further issues.

Best, Yumin

[bio-xtt]

Thank you very much

[bio-xtt]

Hello, I used the following command to construct TE references for other species, and the following error occurred. How should I solve it python3 build_reference.py --species Other --other_species_TE /work/xtt/biosoft/Mmul_10/Macaca_rmsk.csv --other_species_GTF /work/xtt/biosoft/Mmul_10/Macaca_fascicularis.Macaca_fascicularis_5.0.102.gtf

TE file:

GTF file

erorr information:

[Szym29]

Hi @bio-xtt ,

Can you update the code again? I have fixed this issue. Thanks.