Plant genomes fails

[Lcornet]

Dear RM team,

I tried to identify the repeats of my Cassava genome : RepeatMasker -pa 40 -xsmall -dir /outdir/RM cassava/tme3.fasta

The program seems to work perfectly if I look into logs, nevertheless I have only <2% of repeats. This value should be around 70 %. I run the pipeline on Arabidopsis, with 70 % of assess repeats, and I have also 2 %.

Is it due to a bad version of repbase (RepBase2016 (20160829) ) ? Do I have to take another DB for plants ?

Thanks for your help, Luc

[jebrosen]

You can use util/queryRepeatDatabase.pl in the -tree mode to view all of the species and number of repeat families that are covered by your configured libraries. It is possible that a more recent library such as RepBase RepeatMasker edition 20181026 has more repeats in that genome, if you have access to it.

[xiaoyezao]

Dear RM team,

I tried to identify the repeats of my Cassava genome : RepeatMasker -pa 40 -xsmall -dir /outdir/RM cassava/tme3.fasta

The program seems to work perfectly if I look into logs, nevertheless I have only <2% of repeats. This value should be around 70 %. I run the pipeline on Arabidopsis, with 70 % of assess repeats, and I have also 2 %.

Is it due to a bad version of repbase (RepBase2016 (20160829) ) ? Do I have to take another DB for plants ?

Thanks for your help, Luc

Hi Luc,

I have same problem, with only <2% of repeats reported (all are satellites). What's your workaround to solve this?

Tao

[jebrosen]

@xiaoyezao are you using a version of Dfam and/or RepBase that has repeats for the species you ran RepeatMasker on?

You can use util/queryRepeatDatabase.pl in the -tree mode to view all of the species and number of repeat families that are covered by your configured libraries.