diff --git a/PhyloToL-Part-1.md b/PhyloToL-Part-1.md index d61c2a1..94b07ee 100644 --- a/PhyloToL-Part-1.md +++ b/PhyloToL-Part-1.md @@ -54,6 +54,24 @@ And all of the CDS fasta files should be in a folder alongside the [Scripts](htt ## The Hook Database +PhyloToL6 is designed to have an interchangeable hook. As the Hook database is replaceable and customizable, this step offers an opportunity to filter data for a group of gene families/functional groups of interest. + +###Swapping out the hook +What to know about using your own hook: +* +The hook lives in the Databases folder, specifically the db_OG folder +* +The fasta file contains ….. +The diamond file contains ….. +It is recommended that you create your own diamond database using your fasta file, so you can be sure that diamond will be compatible with your computer’s version +To do this, do the following command +diamond makedb --in -d .dmnd +Be aware that you must give your fasta file and your diamond file the same exact name, or else your run will fail at the end +For example, the Katzlab Hook-6.6 files are named: +Hook-6.6.fasta +Hook-6.6.dmnd + + ## Processing transcriptomes