Hi all, I have 2 groups of RNAs, one is the experimental group, the other is the control group. What I need to do is to check if there is some k-mer sequences highly enriched in the experimental group compared to the control group, or vice versa. My question is that,
1) How can I get the RNA sequences from coordinates. I think maybe it is right to use bedtools to extract the FASTA sequences of each exons respectively and then combine them together, and then convert the 'T' in DNA to 'U' in RNA, but is there any method more efficient?
2) Actually I don't know any tools can do such a k-mer comparison between different RNA groups. Could anyone recommend some tools? Thank you so much.