HAMR is a web application that allows you to detect and classify modified nucleotides in RNA-seq data.HAMR scans RNA-sequencing data for sites showing potential signatures of nucleotide modification. Simply point it to your RNA-seq data it will scan the entire transcriptome. You can also limit the analysis to particular genomic regions of interest, either by entering one or providing a BED file containing the intervals. The output is a table containing the list of sites with nucleotide patterns that deviate from expectation at a statistically significant rate.
Wang Lab @ IBI
- R package
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RNA. 2013 Dec;19(12):1684-92. doi: 10.1261/rna.036806.112.
HAMR: high-throughput annotation of modified ribonucleotides.
Ryvkin P, Leung YY, Silverman IM, Childress M, Valladares O, Dragomir I, Gregory BD, Wang LS.