Closed xinshuaiqi closed 5 years ago
Hi Xinshuai,
Thank you for your questions, which may help to clarify things for other users. Please refer to the following information.
gff out file:
LAI output:
-mono
parameter.Repeatability:
You should expect a slight difference (<.1) between runs. Due to the use of multithreading, unfortunately, there isn't a way to control this slight variation for now. For LAI estimation, the correction procedure is set to the quick mode (-q) in LTR_retriever by default, which is to apply a linear estimation of whole-genome LTR identity to accelerate the procedure, instead of performing whole-genome all-versus-all blast of LTR sequences. You may try the latter method to control this potential approximation error.
genome.mod.out
is the RepeatMasker result by using the LTR_retriever produced library to mask the genome.mod
file. genome.mod
is created due to the length of the sequence name >15 characters. Naming length is limited by RepeatMasker so I did the trimming here. Sequences are untouched.
About finder and harvest False positive rate is the percentage of the falsely reported cases. To determine whether an item is false, you need to have a standard set, or true answer, to be compared with. For de novo LTR annotations, if there is no human curation, there is no standard set, thus you can not know the false positive rate. You may curate a subset of the intact LTR-RT to get an insight. Instead, we provide come curated examples in our paper supplementary data to compare different combinations of inputs. You can calculate the false positive rate by using the equations in the method section.
Please let me know if you have further questions.
Thanks, Shujun
Thanks for clarifying these questions! Best, Xinshuai
Hi Shujun, I have a few question while running LAI. I am new to LTR, so I hope you can help me clarify a few things:
gff out file:
1) What's the meaning of
Diversity(%)
andSW_score
in the gff output? 2) And if thesequece-region
has 'INT' as suffix, does that mean "intact LTR"? Better to have an explanation of the Output file in the manual.LAI output:
1) when you calculate the
whole genome raw LAI and LAI
, do you use the mean value of all the scaffolds? what if my input file is a contig file, and many short contigs have no LTR (thus raw LAI and LAI = 0), will that impact on thewhole genome raw LAI and LAI
? 2) I am not fully understand the correction on raw LTR that you mentioned in the paper "LAI score is correlated with the activities of LTR-RT ...". Does this correction has bias between autopolyploid and allopolyploid plants?3) what the decimal number of
Intact
andTotal
mean in the LAI output? Percentage of this LTR in this sequence?Repeatability:
It happen to me that If I run the analysis on the same genome, I may get different LAI score, is that normal? Is that because you used any
seed
in the script?I do get both ".mod.out" and '.out' as output, what's the difference?
About finder and harvest
Is there a way to estimate the
False positive rate
in these two outputs based on your retriever output?