Thank you very much for developing this robust tool to monitor the expression levels of REs!!!
I have a question about the Clean outputs. What's the meaning of column 5 and "divergence" (column 9) [blue box in the figure] for the output bed file? I am interested in genomic loci which are not annotated by RepeatMsker. So, I would like to calculate these expression levels for these specific genomic loci. In this situation, I am considering the possibility to build the bed file like the SQuLRE Clean output bed and calculate the expression levels.
Hello Wan R.,
Thank you very much for developing this robust tool to monitor the expression levels of REs!!!
I have a question about the Clean outputs. What's the meaning of column 5 and "divergence" (column 9) [blue box in the figure] for the output bed file? I am interested in genomic loci which are not annotated by RepeatMsker. So, I would like to calculate these expression levels for these specific genomic loci. In this situation, I am considering the possibility to build the bed file like the SQuLRE Clean output bed and calculate the expression levels.
Thank you so much!
Best,
Zunpeng