update README.md

Author: havu73

README.md

@@ -17,8 +17,6 @@ File structure this folder:
 │   ├── hg38_genome_100_browser.bed.gz
 │   ├── hg38_genome_100_segments.bed.gz
 │   ├── hg38_genome_100_segments_no_regions_mapped_from_multiple_hg19_ucsc.bed.gz
-│   ├── hg38_IHEC_browser.bb
-│   ├── hg38_IHEC_segments.bed.gz
 │   ├── state_annotations_processed.csv
 │   └── trackDb.txt
 ├── hub.txt
@@ -36,10 +34,13 @@ File structure this folder:
 - 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. 
 - Folder <a href="https://public.hoffman2.idre.ucla.edu/ernst/2K9RS/full_stack/full_stack_annotation_public_release/mm10/">mm10</a> contains data of the full-stack annotations generated by training a ChromHMM stacked model on 901 datasets profiling 14 chromatin mark in mouse. This model was introduced in <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02994-x"> manuscript </a>, and <a href="https://github.com/ernstlab/mouse_fullStack_annotations"> Github</a>.
 
+<!-- 
 # Pilot full-stack chromatin state annotations generated using data from IHEC
 - File <a href="https://public.hoffman2.idre.ucla.edu/ernst/2K9RS/full_stack/full_stack_annotation_public_release/hg38/hg38_IHEC_segments.bed.gz">hg38_IHEC_segments.bed.gz</a> contains a simple four-column .bed file for full-stack state annotation in hg38 assembly. This annotation was learned using 5339 datasets released by <a href="https://epigenomesportal.ca/ihec/">IHEC</a>. The fourth column contains a state label with a prefix number that can be used to order the states. The OverlapEnrichment and NeighborhoodEnrichment commands of ChromHMM with the '-labels' option can compute enrichments for this file and order states based on the prefix number.
 - Right now, the state names and characterizations are **tentative** and are subject to changes. The tentative state characterizations can be downloaded from <a href="https://github.com/ernstlab/full_stack_ChromHMM_annotations/tree/main/pilot_IHEC/IHEC_state_annotations.xlsx">IHEC_state_annotations.xlsx</a>.  
 
+-->
+
 # UCSC genome browser tracks
 - To view the full-stack annotation in hg19, hg38 and mm10, including the pilot annotation learned using IHEC data, please use the track hub link https://public.hoffman2.idre.ucla.edu/ernst/2K9RS//full_stack/full_stack_annotation_public_release/hub.txt. Instructions on how to view these tracks on UCSC Genome Browser is provided in a step-by-step <a href="https://github.com/ernstlab/mouse_fullStack_annotations/view_ucsc_genome_browser.pptx"> powerpoint</a>.