Questions about *.pass.list #29
Labels
Comments
|
Hi Jiahe, This is the same element which is likely a genuine LTR element. One of the TSDs was not converted to the complementary form due to the ambiguity of direction. I have fixed this minor bug in the later updated version. Thanks for using LTR_retriever! Cheers, |
oushujun
added a commit
that referenced
this issue
Dec 4, 2018
… locates at the boundary of a contig. 2. fix the bug #28 #29 for sometimes pruducing slightly different results when using both LTRharvest and LTR_FINDER inputs. 3. fix the bug #28 for biased recognition of TGCA motif over non-TGCA motifs. This fix produced similar prediction quality in terms of sensitivity, specificity, accuracy, and precision that were tested in genomes of sacred lotus and rice.
oushujun
added a commit
that referenced
this issue
Dec 4, 2018
…s when using both LTRharvest and LTR_FINDER inputs.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Hi Shujun,
From the log file, i know *.pass.list contain the whole genome LTR-RTs (redundant). I found some LTR-RT have the same coordinate with different TSD.
C01:2584769..2588663 pass motif:TGCA TSD:ATTAC 2584764..2584768 2588664..2588668 IN:2585668..2587763 0.9911 ? unknown NA 344355
C01:2584769..2588663 pass motif:TGCA TSD:GTAAT 2584764..2584768 2588664..2588668 IN:2585668..2587763 0.9911 - unknown NA 344355
I don't know why this happens. Are both results reliable LTR-RTs?
Best,
Jiahe
The text was updated successfully, but these errors were encountered: