Hi,
I came across this tool: https://bioconductor.riken.jp/packages/3.7/bioc/manuals/exomePeak/man/exomePeak.pdf
I have non-fragmented libraries (meaning the RNA was not fragmented before sequencing). This means many tools like macs2 etc cannot be used. But can I use exomePeak? I went over the manual, and it seems to expect fragmented data, but I was not sure...
* edit * The data I have are sequenced reads (fastq files) that I have aligned to the reference genome. The original RNA was long, as it was not fragmented, but the read length is about 100bp. I want to check for enrichment of genes in this data.
I had done this in one other way - I aligned and calculated FPKM, removed lowest quartile and then calculated FC change for each gene in my data to find genes enriched FC>=4 in IP vs. input.
It was suggested to me that exomepeak would be a better tool for such analysis, and I am not sure from the manual if the lack of fragmentation excludes my files from this tool.
Thanks for your input,
