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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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DNA type transposons cannot be classified? #15

Closed hechuweiran closed 3 years ago

hechuweiran commented 3 years ago

HI sorry to bother you. I want to use TEsorter to classify transposons that Repeatmodeler fails to classify, but the results show that the software seems to be unable to classify transposons of DNA type. DNA type transposons cannot be classified?

Chr1A:3671..3701|rnd-1_family-759#Unknown Chr1A:3671..3701|rnd-1_family-759#DNA/hAT Chr1A:3702..3972|rnd-1_family-759#Unknown Chr1A:3702..3972|rnd-1_family-759#DNA/hAT Chr1A:4491..4586|rnd-1_family-544#Unknown Chr1A:4491..4586|rnd-1_family-544#DNA/hAT-Ac Chr1A:15383..15535|rnd-1_family-544#Unknown Chr1A:15383..15535|rnd-1_family-544#DNA/hAT-Ac Chr1A:19859..20089|rnd-5_family-3147#Unknown Chr1A:19859..20089|rnd-5_family-3147#DNA/PIF-Harbinger Chr1A:23324..23637|rnd-1_family-2#Unknown Chr1A:23324..23637|rnd-1_family-2#DNA/PIF-Harbinger Chr1A:24437..24541|rnd-6_family-12487#Unknown Chr1A:24437..24541|rnd-6_family-12487#DNA/hAT-Tip100 Chr1A:27373..27686|rnd-1_family-2#Unknown Chr1A:27373..27686|rnd-1_family-2#DNA/PIF-Harbinger Chr1A:28495..28592|rnd-6_family-12487#Unknown Chr1A:28495..28592|rnd-6_family-12487#DNA/hAT-Tip100 Chr1A:29927..29982|rnd-1_family-658#Unknown Chr1A:29927..29982|rnd-1_family-658#DNA/TcMar-Stowaway Chr1A:30124..30220|rnd-1_family-658#Unknown Chr1A:30124..30220|rnd-1_family-658#DNA/TcMar-Stowaway Chr1A:30360..30608|rnd-1_family-7#Unknown Chr1A:30360..30608|rnd-1_family-7#DNA/PIF-Harbinger Chr1A:31505..31617|rnd-5_family-139#Unknown Chr1A:31505..31617|rnd-5_family-139#DNA/PIF-Harbinger Chr1A:31644..31689|rnd-5_family-139#Unknown Chr1A:31644..31689|rnd-5_family-139#DNA/PIF-Harbinger Chr1A:34307..34569|rnd-5_family-2428#Unknown Chr1A:34307..34569|rnd-5_family-2428#DNA/PIF-Harbinger Chr1A:35672..35780|rnd-5_family-1497#Unknown Chr1A:35672..35780|rnd-5_family-1497#DNA/PIF-Harbinger Chr1A:36038..36284|rnd-5_family-6489#Unknown Chr1A:36038..36284|rnd-5_family-6489#DNA/PIF-Harbinger

zhangrengang commented 3 years ago

Which -db do you use? TEsorter is able to classify DNA TEs with rexdb (but not with gydb). TEsorter is based on protein domains. But Repeatmodeler generate consensus library for repeat masking. The consensus sequence might break coding frame (frame shift), which may lead to failure of TEsorter.