search

oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
176 stars 40 forks source link

truncted LTR #96

Closed xiaoyezao closed 3 years ago

xiaoyezao commented 3 years ago

Hi Shujun,

I am wondering is it possible to generate the truncated LTR list like what solo_finder.pl does?

Another question is that in the log file, it says:

Thu Apr 29 18:24:01 CST 2021    3962 truncated LTR-RTs found
Thu Apr 29 19:07:05 CST 2021    233 truncated LTR sequences have added to the library

Why most truncated LTRs were filtered out and what's the criteria used for filtering?

Bests,

Karl

oushujun commented 3 years ago

Hi Karl,

You may minus solo and intact LTRs and the rest are truncated. If you have a particular definition of truncated LTR, you need to set up your own filters.

Most truncated LTRs have corresponding intact versions. Only the novel truncated LTR sequences are retained in the library.

Shujun

On Wed, Jun 16, 2021 at 2:17 PM xiaoyezao @.***> wrote:

Hi Shujun,

I am wondering is it possible to generate the truncated LTR list like what solo_finder.pl does?

Another question is that in the log file, it says:

Thu Apr 29 18:24:01 CST 2021 3962 truncated LTR-RTs found Thu Apr 29 19:07:05 CST 2021 233 truncated LTR sequences have added to the library

Why most truncated LTRs were filtered out and what's the criteria used for filtering?

Bests,

Karl

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/96, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NH3KCYZVUF4QEUKFKTTTA6VXANCNFSM46YV66GA .

xiaoyezao commented 3 years ago

From which file to minus solo and intact LTRs? Is it .LTRlib.redundant.fa ?

Thank you Shujun.

oushujun commented 3 years ago

Hello, it should be the whole genome annotation, so the gff3 file.

Shujun

On Sun, Jun 20, 2021 at 11:42 AM xiaoyezao @.***> wrote:

From which file to minus solo and intact LTRs? Is it .LTRlib.redundant.fa ?

Thank you Shujun.

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/96#issuecomment-864494997, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGTT2FKKETEKTAQNBLTTVPTRANCNFSM46YV66GA .