Merge branch 'main' of https://github.com/ernstlab/full_stack_ChromHMM_annotations

Author: havu73

README.md

@@ -8,6 +8,7 @@ Within this folder:
 - File <a href="https://public.hoffman2.idre.ucla.edu/ernst/2K9RS//full_stack/full_stack_annotation_public_releasehg19_genome_100_browser.bed.gz">hg19_genome_100_browser.bed.gz</a> contains a browser file of full-stack state annotation in hg19 assembly. This file is compatible to for UCSC genome browser. Since our training data (1032 input data tracks) are in hg19, the assembly used for original training and annotation.
 - File <a href="https://public.hoffman2.idre.ucla.edu/ernst/2K9RS//full_stack/full_stack_annotation_public_releasehg38lift_genome_100_segments.bed.gz">hg38lift_genome_100_segments.bed.gz</a> is similar to hg19_genome_100_segments.bed.gz, but based on a liftOver of each 200bp bin to hg38. Positions mapped to from multiple locations in hg19 did not receive an annotation. Since the 200-bp intervals are no longer maintained when using OverlapEnrichment and NeighborhoodEnrichment the options '-b' and '-lowmmem' should be used with this command in addition to the '-labels' option as with the hg19 file.
 - File <a href="https://public.hoffman2.idre.ucla.edu/ernst/2K9RS//full_stack/full_stack_annotation_public_releasehg38lift_genome_100_browser.bed.gz">hg38lift_genome_100_browser.bed.gz</a> is similar to hg19_genome_100_browser.bed.gz but is for the liftOver to hg38. Positions mapped to from multiple locations in hg19 did not receive an annotation.
+
 - Detailed description of states can be found at Additional File 3 in the  <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02572-z"> manuscript </a>. If you want a csv file outline similar information about the states' desctiptions, you can also use file ```state_annotations_processed.csv``` provided in this folder. 
 
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