MGEScan nonLTR - identified features extend beyond length of scaffold

[mcsimenc]

Hi Hyungro

I ran MGEScan nonLTR locally not within galaxy. My nonLTR nonltr.gff3 output has a few features whose end coordinate is beyond the end of the sequence it is on. Any idea why this might be happening? I am not sure if it is safe to ignore or if this could indicate that potentially all the features in the gff3 are in the wrong place.

Thanks!!
Matt Simenc

[lee212]

I think I need to run a test. Could you provide me a sample input sequence with your gff3 output? That would be helpful to debug the issue. Thanks!

[mcsimenc]

Correction: I used mgescan ltr: here's the call

mgescan ltr ./Sacu_asm_separated_scafs --mpi=20 --output=./output 1>mgescan.out 2>mgescan.err

Here's the questionable annotation:

Sacu_v1.1_s0041 MGEScan_nonLTR mobile_genetic_element 1165493 1170362 . . . ID=Sacu_v1.1_s0041.fa_1165493

The sequence:

Sacu_v1.1_s0041.fa.zip

Unfortunately, since I ran this, the cluster I use underwent upgrades and mgescan was not reinstalled properly so I can't run it again right now.

[madelhorius]

Hi Hyungro
I have the same issue, nonltr.gff3 includes some elements that end beyond the end of the scaffold they are on. How did you solve that issue?
Btw. do you have experience with the identification of LINEs in plants? Do you know if your software is able to identify LINEs in plants, too?
Thanks for your reply!
Marius

[lee212]

Hi Marius,

No, I did not fix this issue, this is still open. I probably have to replicate your issue with a sample dataset, if you could share with me. Then I can start debugging the problem that you encountered, and this is related to MGEScan_nonLTR, not LTR? I am not certain you can use this tools for LINES in plants but I might ask around to my colleagues.

[madelhorius]

Thank you for getting back to me! I sent you a sample dataset per email. Hopefully this issue can be solved.

[lee212]

Hi Marius,

hmm, I haven't received the email, could you resend to my school account lee212 at indiana.edu?