zhenlisme/heliano

HELIANO is a software for detection and classification of Helitron-like elements.

heliano's Issues

Do we need RepeatMasker with RC.representative.fa after HELIANO running

Hi, @Zhenlisme

Thanks for this nice tool! I am just curious about the postprocessing of Heliano output. Should we use RC.representativate.fa for RepeatMasker to get an estimation of the fragmented one? Or RC.representativate.bed should be the result I should use to complementary with other TEs annotation gff (such as EDTA, RepeatModeler2)

Question: Evalue cutoffs for HELIANO

Hi @Zhenlisme,

Super cool tool, and great paper to go with it! I just had a question about the E-value cutoffs used in HELIANO.

My understanding was that a lower Evalue was better, for example with an Evalue of 0.001 being worse than 0.00001 (ie a lower chance of finding the sequence by random chance). In the main python script, it looks like sequences are filtered out if they have an Evalue lower than 1e-5 (0.00001). Does this mean that sequences with very low Evalues are filtered out? Should it be sequences with Evalues higher than 1e-5 that are removed?

E.g Line 260-262 in the main script:

c_evalue, i_evalue = splitlines[11:13]
                if float(c_evalue) > 1e-5 or float(i_evalue) > 1e-5:
                    continue

Maybe I misunderstood how this is filtered too, so apologies in advance if I have got confused!

Thanks!