Repeat_annotation/ ltr_finder

[anxuan-web]

Hi!
I encountered an error following your steps: "open fasta.1 error!"

##This step predict the LTR;Input file is fasta file;Output file is the ltr_finder file;
ltr_finder -w 2 -s LTR_FINDER.x86_64-1.0.5/tRNAdb/Bos_taurus.tRNA.fa fasta.1 1>fasta.1ltr_finder

So, I want to know what this parameter means: "fasta.1 1", and how to solve.

Best wishes!

[YinYuan-001]

The fasta.1 is ​genome file in fasta format that you wanted to annotate. The "open fasta.1 error" might be caused by the wrong genome file with nnacceptable format, incorrect name or file path.

You can use the "ltr_finder -h" command to ​get more helpful information like below:

ltr_finder -h
ltr_finder v1.05
Usage : [options] <INPUT_FASTA_FILE>
-o NUM gap open penalty, default is 3
-t NUM gap extension penalty, default is 1
-e NUM gap end penalty, default is 1
-m NUM match score, default is 2
-u NUM unmatch score, default is -2
-D NUM Max distance between 5'&3'LTR, default is 20000
-d NUM Min distance between 5'&3'LTR, default is 1000
-L NUM Max length of 5'&3'LTR, default is 3500
-l NUM Min length of 5'&3'LTR, default is 100
-p NUM min length of exact match pair, default is 20

Hope my response is helpful to you.

[anxuan-web]

Thank you for your help. I succeeded in solving the problem.
Best wishes!