mengzhou / monomerannotation

Source codes and scripts for monomer detection and subtype classification

MonomerAnnotation

Source codes and scripts for monomer detection and subtype classification

Contents

1. detection: the package of programs used for monomer detection.
2. classification: the scripts used for monomer subtype classification.
3. results: the detection and classification results of the three major monomer subtypes, A, G, and T in the mm10 genome.

monomerannotation's Issues

Usage of program and memory issue

Hello,

First thank you for your work. I would like to test your tool on other sub-families of transposable elements so I'm trying to follow the instructions but I have some questions.

I have a single multi-fasta with mm10 genome, multiple fasta with individual chromsomes and a MUSCLE alignment of my list of transposable elements in ClustalW format.

So I ran the construct tool first and then, when trying scan, by providing the complete genome (or just 1 chromosome), the program kill itself. By checking the memory, I saw that it reached +200gb of RAM. I tested with chrF.fa and train.aln, the program worked well. So I think the fasta files are too big for the program (1.18gb for the complete genome, 60-200mb for the individual chromosomes). So I would like to know if there is a way to do it on the whole genome ?

Also, do the scripts in the directory pipeline have to be run after construct and scan or is it a totally separate part ?

The exact commands that I used are (here with the toy_test files):
construct -o train.construct.model -u -v train.aln
scan -o train.scan.bed -v -c chrF.fa train.construct.model

Thank you for your time and your work.

Best.

Pierre-Emmanuel