Add Homer uniqmap

[edmundmiller]

Generating uniqmap

Unfortunately, generating your own uniqmap files is a clunky procedure. However, you can do it by following these steps:

1. Place the genome FASTA files for the genome of interest in a directory. There MUST be only one entry per file (i.e. chr1.fa, chr2.fa, chr3.fa). Unfortunately, the programs will not accept a single FASTA file will all of the chromosomes.
2. Next, run the getMappableRegions command. This will eat up a ton of memory, which can be scaled by adjusting the first argument which sets the number of sequences that are analyzed in parallel. The program takes a while on mammalian genomes (~day). The second argument is the length of the reads you want to consider unique: "getMappableRegions 1000000000 50 *.fa > out.50nt.txt"
3. Next run a utility program to create the uniqmap directory: "homerTools special uniqmap uniqmapDirectory/ out.50nt.txt". The "uniqmapDirectory/" can then be used with the findPeaks command.

Source

Might be useful for Nascent, I don't know if anything besides GRO-Seq uses it.

[edmundmiller]

Implemented in https://github.com/Functional-Genomics-Lab/homer-uniqmap-nf

Probably a better place for it, as it's pretty niche. If anyone needs any help, feel free to comment here, open an issue at homer-uniqmap-nf or find me in the Nascent channel of the nf-core slack!