Agnieszka Golicz

For the file: TE-type.consensus.fa and TE_copies_with_flank.fa Per repeat masker documentation: https://www.animalgenome.org/bioinfo/resources/manuals/RepeatMasker.html The recommended format for IDs in a custom library is: >repeatname#class/subclass or simply >repeatname#class I just wanted to confirm...

Ok, thanks that makes sense. I will try to give it a try in January.

Hi, I have been having the same issue, but neither -n5, -n10 or -xasm20 have helped. Could it be due to very large chromosomes. Some of the chromosomes exceed 2Gb...

Thanks! I assume 2147483647 is the upper limit? Mapping short contigs to long chromosomes works fine, but aligning two long chromosomes fails. I can just split them to avoid hitting...