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Hello,
I am trying to identify and quantify retrotransposon expression in my experimental RNA-seq data sets. Being a newbie, I'm only aware of 2 potential ways to approach this problem;
1. RepeatMasker has a nice output Table of different retrotransposon classes detected in fasta files but it seems like a tremendous waste of time and effort to run that program just to obtain the final analysis file.
2. Index a genome using the RepeatMaskerViz gtf from UCSC, and then align against that genome.
Ideally I would like to assess differences at the level of class, order and at the individual unique retrotransposon level. I'd greatly appreciate any suggestions.
Thank you in advance.
I am trying to identify and quantify retrotransposon expression in my experimental RNA-seq data sets. Being a newbie, I'm only aware of 2 potential ways to approach this problem;
1. RepeatMasker has a nice output Table of different retrotransposon classes detected in fasta files but it seems like a tremendous waste of time and effort to run that program just to obtain the final analysis file.
2. Index a genome using the RepeatMaskerViz gtf from UCSC, and then align against that genome.
Ideally I would like to assess differences at the level of class, order and at the individual unique retrotransposon level. I'd greatly appreciate any suggestions.
Thank you in advance.