Using Custom Libraries in RepeatMasker

[gprakhar]

Hello,

I am using RepeatMasker with custom plant repeat libraries, on the newly sequenced Neem plant genome.
My question is, in the logfile why does RepeatMasker say that,
"Checking for E. coli insertion elements"

When I have not explicitly asked it to look for that?
I run it using the command,
$RepeatMasker -lib <lib-name.fa> <scaffold_file.fa>

Thanking you,
--
Prakhar Gaur

[Wurstmensch]

Because it checks in default mode for them. When you want to skip the insertion elements check, you have to give the option -no_is in your string.

[gprakhar]

Hi,

Thank you for the clarification.

Regards,
--
pg