scTE building customs reference index ERROR !

[akui113]

Hi, @jphe it's the best tool! I also encountered the same problem as #3，but the species is Macaca mulatta. gene annotation file was downloaded from http://ftp.ensembl.org/pub/release-104/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.104.gtf.gz, and repeatmask file was downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/rheMac10/database/rmsk.txt.gz .

Then, I transformed the repeatmask file into a six-column bed file with the option awk 'BEGIN{FS=OFS="\t"}{print $6,$7,$8,$11,$3,$10}' rmsk.txt > mmul10rmsk.bed and make sure the chromosome name consistent with gene annotation file. Lastly, I building the index scTE_build -te mmul10rmsk.bed -gene Macaca_mulatta.Mmul_10.104.gtf -o Mmul_10scTE.idx. However, I get the ERROR : Counting genome other not supported.

Any tips are appreciated ! Thank you for your generous help!

[jphe]

I feel this issue has been fixed before, it works fine in my PC with your code, can you update the scTE and try again?

[akui113]

@jphe wow! yes ! Thank you for your generous helping!