xvazquezc / genome_annotation_with_maker2 Goto Github PK

Hi xvazquezc,

Thank you for having your repeat library construction pipeline public, it has been super helpful!

I have one question regarding the protocol: I have been successful in identifying MITEs in my fungal genome, and I have proceeded to identify LTRs. However, when I try to identify candidate elements for recent LTRs, the resulting gff99 file is empty, so I cannot go forward. I assumed that was because perhaps my data-set didn't have any, but I am not sure if this is true (there were not any errors reported). I then moved on to identified older LTRs, which produced a gff85 with data.
At some point in the pipeline, we need to run:
perl ${DIR_CRL}/cleanRM.pl ${PREFIX}.outinner85.out ${PREFIX}.outinner85.masked > ${PREFIX}.outinner85.unmasked

However, in my case this does not work because i had no 99 output and it seems that cleanRM.pl requires it. So, I am confused as to how to proceed, which are my unmasked and cleaned files?

Thank you so much!

L.