diff --git a/.gitignore b/.gitignore
index f52b0de..950912c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 #PyCharm workdir
 .idea
-
+*.pyc
 #Scripts output directory content
-output/*
+output/*.json
diff --git a/IHEC_json_converter/bisulfite.py b/IHEC_json_converter/bisulfite.py
index 6997f13..ee16540 100755
--- a/IHEC_json_converter/bisulfite.py
+++ b/IHEC_json_converter/bisulfite.py
@@ -1,29 +1,21 @@
 __author__ = 'kelley'
 
-import json
-from general import convert_to_IHEC_format
 
 VERSION='1.6'
 
-def bisulfite_wrapper(assembly, taxon_id):
-    url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=whole-genome%20shotgun%20bisulfite%20sequencing'
+# Used to set is_main
+BISULFATE_TRACK_HIEARCHY = {'methylation_profile': ['methylation state at CpG', 'signal']}
 
-    # Used to set is_main
-    track_hierarchy = {'methylation_profile': ['methylation state at CpG', 'methylation state at CHH']}
 
-    def dataset_additions_f(experiment, json_object):
+def bisulfate_addition(experiment, json_object):
+    #Set experiment_type
+    json_object['experiment_attributes']['experiment_type'] = 'DNA Methylation'
+    json_object['experiment_attributes']['assay_type'] = 'WGB-Seq'
 
-        #Set experiment_type
-        json_object['experiment_attributes']['experiment_type'] = 'DNA Methylation'
-        json_object['experiment_attributes']['assay_type'] = 'WGB-Seq'
+    return json_object
 
-        return json_object
 
-    return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f)
-
-
-
-if __name__ == "__main__":
-    data = bisulfite_wrapper(assembly='hg19', taxon_id=9606)
-    with open('../output/bisulfite_v%s.json' % VERSION, 'w+') as outfile:
-        json.dump(data, outfile, indent=4)
\ No newline at end of file
+# if __name__ == "__main__":
+#     data = bisulfite_wrapper(assembly='hg19', taxon_id=9606)
+#     with open('../output/bisulfite_v%s.json' % VERSION, 'w+') as outfile:
+#         json.dump(data, outfile, indent=4)
\ No newline at end of file
diff --git a/IHEC_json_converter/chipseq.py b/IHEC_json_converter/chipseq.py
index 65b9ce5..b624cd9 100755
--- a/IHEC_json_converter/chipseq.py
+++ b/IHEC_json_converter/chipseq.py
@@ -1,34 +1,26 @@
 __author__ = 'kelley'
 
-import json
-from general import convert_to_IHEC_format
 
 VERSION='1.6'
 
-def chip_seq_wrapper(assembly, taxon_id, target):
-    url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=ChIP-seq&target.name=%s-human' % target
-
-    # Used to set is_main
-    track_hierarchy = {'peak_calls': ['optimal idr thresholded peaks', 'conservative idr thresholded peaks',
+CHIPSEQ_TRACK_HIEARCHY = {'peak_calls': ['optimal idr thresholded peaks', 'conservative idr thresholded peaks',
                                 'replicated peaks', 'peaks', 'hotspots'],
                            'signal': ['signal p-value', 'fold change over control', 'signal', 'raw signal']}
 
-    def dataset_additions_f(experiment, json_object):
-
-        #Set experiment_type
-        json_object['experiment_attributes']['experiment_type'] = experiment['target']['label']
 
-        return json_object
+def chip_seq_addition(experiment, json_object):
 
-    return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f)
+    #Set experiment_type
+    json_object['experiment_attributes']['experiment_type'] = experiment['target']['label']
 
+    return json_object
 
 
 
 
-if __name__ == "__main__":
-    targets = ['H3K27ac', 'H3K27me3', 'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3']
-    for t in targets:
-        data = chip_seq_wrapper(assembly='hg19', taxon_id=9606, target=t)
-        with open('../output/%s_v%s.json' % (t, VERSION), 'w+') as outfile:
-            json.dump(data, outfile, indent=4)
+# if __name__ == "__main__":
+#     targets = ['H3K27ac', 'H3K27me3', 'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3']
+#     for t in targets:
+#         data = chip_seq_wrapper(assembly='hg19', taxon_id=9606, target=t)
+#         with open('../output/%s_v%s.json' % (t, VERSION), 'w+') as outfile:
+#             json.dump(data, outfile, indent=4)
diff --git a/IHEC_json_converter/fetch_all_exp_jsons.py b/IHEC_json_converter/fetch_all_exp_jsons.py
index e646b8f..e2c08fc 100755
--- a/IHEC_json_converter/fetch_all_exp_jsons.py
+++ b/IHEC_json_converter/fetch_all_exp_jsons.py
@@ -2,7 +2,7 @@
 import getopt
 import json
 from datetime import datetime
-import rnaseq, bisulfite, chipseq
+from reference_epigenome_experiments import collect_experiments
 
 def main(argv):
     opts, args = getopt.getopt(argv, "", ["assembly=", "taxon-id="])
@@ -22,43 +22,9 @@ def main(argv):
 
     date_str = datetime.now().date()
 
-    #Todo: Merge experiments as a single JSON
-
-    #Whole-Genome Bisulfite Sequencing experiments
-    print("Processing WGB-Seq...")
-    try:
-        data = bisulfite.bisulfite_wrapper(assembly='hg19', taxon_id=9606)
-        filename = 'WGB-Seq_%s_%s_%s.json' % (taxon_id, assembly, date_str)
-        output_file(data, filename)
-        print("Done.")
-    except Exception as e:
-        print('An error occured while fetching WGB-Seq experiments: ' + e.message)
-    print
-
-    #RNA-Sequencing experiments
-    print("Processing RNA-Seq...")
-    try:
-        data = rnaseq.rna_seq_wrapper(assembly=assembly, taxon_id=taxon_id)
-        filename = 'RNA-Seq_%s_%s_%s.json' % (taxon_id, assembly, date_str)
-        output_file(data, filename)
-        print("Done.")
-    except Exception as e:
-        print('An error occured while fetching RNA-Seq experiments: ' + e.message)
-    print
-
-    #ChIP-Seq experiments
-    targets = ['H3K27ac', 'H3K27me3', 'H3K36me3', 'H3K4me1', 'H3K4me3', 'H3K9me3']
-    for t in targets:
-        print("Processing ChIP-Seq %s..." % t)
-        try:
-            data = chipseq.chip_seq_wrapper(assembly='hg19', taxon_id=9606, target=t)
-            filename = 'ChIP-Seq_%s_%s_%s_%s.json' % (taxon_id, assembly, t, date_str)
-            output_file(data, filename)
-            print("Done.")
-        except Exception as e:
-            print('An error occured while fetching ChIP-Seq %s experiments: ' % t + e.message)
-        print
-    print("Operation completed.")
+    filename = 'ENCODE.{}.{}.{}.json'.format(taxon_id, assembly, date_str)
+    data = collect_experiments(assembly, taxon_id)
+    output_file(data, filename)
 
 
 
diff --git a/IHEC_json_converter/general.py b/IHEC_json_converter/general.py
index be983f7..66e1b56 100755
--- a/IHEC_json_converter/general.py
+++ b/IHEC_json_converter/general.py
@@ -1,12 +1,17 @@
-f__author__ = 'kelley'
+from __future__ import print_function
 
+f__author__ = 'kelley'
 
 import sys
-import urlparse
+from urllib.parse import urlparse
 import requests
 import json
 import os
 from datetime import datetime
+from rnaseq import *
+from bisulfite import *
+from chipseq import *
+
 
 '''
 This file contains methods that convert ENCODE data (from its webservice urls) into JSON that IHEC then loads.
@@ -59,27 +64,11 @@
 # This code is used to generate IHEC json objects from any type of ENCODE assay. Anything assay-specific belongs
 # in other files.
 
-def convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, assay_specific_additions, limit='all'):
-    #Prepare the url - make sure it has the right parameters.
-    url = prep_query_url(url, assembly, taxon_id, limit=limit)
-
-    #Get json response
-    json_response = get_json_from_encode(url)
-
-    if len(json_response) == 0:
-        raise Exception('This url returns no data.')
-
+def convert_to_IHEC_format(datasets, assembly, taxon_id):
+ 
     #Create hub description
     hub_description = create_hub_description(assembly, taxon_id)
 
-    #Create all of the datasets (one for each experiment, sample_id pair)
-    print '%d experiments returned from this query.' % len(json_response)
-
-    datasets = dict()
-    for entry in json_response:
-        datasets.update(create_datasets(entry, assay_specific_additions))
-
-    print '%d IHEC datasets created.' % len(datasets)
 
     # Merge datasets. We can merge two datasets if either
     # 1. they have the same experiment_id and their sample_attributes are identical
@@ -94,13 +83,14 @@ def convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, assay_speci
         experiment_id_to_datasets[experiment_id].append(dataset)
 
     datasets = dict()
-    for experiment_id, these_datasets in experiment_id_to_datasets.iteritems():
+    for experiment_id, these_datasets in experiment_id_to_datasets.items():
         if is_match_sample_attributes([x['sample_attributes'] for x in these_datasets]):
-            print 'Match found: ' + experiment_id
+            print('Match found: ' + experiment_id)
 
             dataset = these_datasets[0]
             dataset['browser'] = merge_tracks(these_datasets)
             dataset['sample_attributes']['sample_id'] = '-'.join(sorted([x['sample_attributes']['sample_id'] for x in these_datasets]))
+            dataset['analysis_attributes'] = create_analysis_attributes(dataset)
             datasets[experiment_id] = dataset
         else:
             for dataset in these_datasets:
@@ -109,7 +99,7 @@ def convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, assay_speci
     # Merge 2
     group_key_to_datasets = dict()
     nogroup_datasets = dict()
-    for accession, dataset in datasets.iteritems():
+    for accession, dataset in datasets.items():
         if dataset['award'] == 'ENCODE3':
             key = (dataset['experiment_attributes']['experiment_type'], dataset['sample_attributes']['sample_id'])
             if key not in group_key_to_datasets:
@@ -119,9 +109,9 @@ def convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, assay_speci
             nogroup_datasets[accession] = dataset
 
     datasets = dict(nogroup_datasets)
-    for key, these_datasets in group_key_to_datasets.iteritems():
+    for key, these_datasets in group_key_to_datasets.items():
          if len(these_datasets) > 1:
-            print 'Collapsed: ', key, len(these_datasets)
+            print('Collapsed: ', key, len(these_datasets))
 
             dataset = these_datasets[0][1]
             dataset['browser'] = collapse_tracks([x[1] for x in these_datasets])
@@ -130,31 +120,66 @@ def convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, assay_speci
              datasets[these_datasets[0][0]] = these_datasets[0][1]
 
     #Set is_main on tracks
-    for accession, dataset in datasets.iteritems():
+    for accession, dataset in datasets.items():
         for track_type in set(signal_mapping.values()):
             if track_type in dataset['browser']:
-                set_main_track(dataset['browser'][track_type], track_hierarchy[track_type], accession, track_type)
+                track_hierarchy = determine_track(dataset)
+                if track_hierarchy:
+                    set_main_track(dataset['browser'][track_type], track_hierarchy[track_type], accession, track_type)
 
 
     # Remove extra entries:
-    for accession, dataset in datasets.iteritems():
+
+    samples = dict()
+
+    for accession, dataset in datasets.items():
         del dataset['award']
         del dataset['accession']
         del dataset['sample_attributes']['replicate']
+        dataset['sample_id'] = dataset['sample_attributes']['sample_id']
+        samples[dataset['sample_id']] = dataset['sample_attributes']
+        del dataset['sample_attributes']
 
-    print '%d IHEC datasets created after merge.' % len(datasets)
+    print('%d IHEC datasets created after merge.' % len(datasets))
 
     return {
         'hub_description': hub_description,
-        'datasets': datasets
+        'datasets': datasets,
+        'samples': samples
     }
 
 
+def determine_addition(experiment_obj):
+    assay_term_name = experiment_obj['assay_term_name']
+    if assay_term_name == 'ChIP-seq':
+        return chip_seq_addition
+    elif assay_term_name == 'RNA-seq':
+        return rna_seq_addition
+    elif assay_term_name == 'whole-genome shotgun bisulfite sequencing':
+        return bisulfite_addition
+
+
+def determine_track(dataset):
+    assay_term_name = dataset['experiment_attributes']['assay_type']
+    if assay_term_name == 'ChIP-seq':
+        return CHIPSEQ_TRACK_HIEARCHY
+    elif assay_term_name == 'RNA-seq':
+        return RNASEQ_TRACK_HIEARCHY
+    elif assay_term_name == 'whole-genome shotgun bisulfite sequencing':
+        return BISULFATE_TRACK_HIEARCHY
+
+def get_epirr_id(item):
+    for registry_id in item['dbxrefs']:
+            if 'IHEC' in registry_id:
+                return registry_id
+    return None
+
+
 def merge_tracks(datasets):
     # We want to merge these datasets together, so we need to merge tracks.
     new_tracks = {}
     for dataset in datasets:
-        for track_type, tracks in dataset['browser'].iteritems():
+        for track_type, tracks in dataset['browser'].items():
             if track_type not in new_tracks:
                 new_tracks[track_type] = []
 
@@ -164,14 +189,14 @@ def merge_tracks(datasets):
 
     #If a track has been assigned to multiple replicates, we might end up seeing it twice - check for that
     cleaned_tracks = dict()
-    for track_type, tracks in new_tracks.iteritems():
+    for track_type, tracks in new_tracks.items():
         url_to_track = dict()
         for track in tracks:
             if track['big_data_url'] not in url_to_track:
                 url_to_track[track['big_data_url']] = []
             url_to_track[track['big_data_url']].append(track)
 
-        for url, url_tracks in url_to_track.iteritems():
+        for url, url_tracks in url_to_track.items():
             if len(url_tracks) > 1:
                 track = url_tracks[0]
                 track['subtype'] = track['subtype'][0:track['subtype'].index('(rep')-1]
@@ -183,7 +208,7 @@ def collapse_tracks(datasets):
     # We want to collapse these datasets together, so we need to collapse tracks.
     new_tracks = {}
     for dataset in datasets:
-        for track_type, tracks in dataset['browser'].iteritems():
+        for track_type, tracks in dataset['browser'].items():
             if track_type not in new_tracks:
                 new_tracks[track_type] = []
             new_tracks[track_type].extend(tracks)
@@ -199,15 +224,13 @@ def create_hub_description(assembly, taxon_id):
     }
 
 
-def create_datasets(experiment, assay_specific_additions):
-    print experiment['accession']
-    experiment = get_json_from_encode('https://www.encodeproject.org/experiments/%s/?format=json' % experiment['accession'])
+def create_datasets(experiment, registry_id, assay_specific_additions):
 
     #Create sample_attributes
     sample_attributes = [create_sample_attribute(replicate) for replicate in experiment['replicates']]
 
     #Create experiment_attributes
-    experiment_attributes = create_experiment_attributes(experiment)
+    experiment_attributes = create_experiment_attributes(experiment, registry_id)
 
     #Create tracks
     datasets = dict()
@@ -266,7 +289,7 @@ def set_main_track(tracks, track_hierarchy, exp_accession, track_type):
 
     #Set main track
     if main_track is None:
-        print 'Dataset %s has no %s tracks.' % (exp_accession, track_type)
+        print('Dataset %s has no %s tracks.' % (exp_accession, track_type))
     else:
         main_track['is_main'] = True
     return tracks
@@ -286,7 +309,7 @@ def create_track(file, protocol_document_href, replicate_num):
                         "subtype": file['output_type']
                     }
         else:
-            print 'Output type not found: ' + file['output_type']
+            print('Output type not found: ' + file['output_type'])
 
 
 def is_match_sample_attributes(sample_attributes):
@@ -311,7 +334,7 @@ def create_sample_attribute(replicate):
     elif biosample['biosample_term_id'].startswith('NTR'):
         sample_ontology_uri = ''
     else:
-        print 'Could not find url for sample ontology %s' % biosample['biosample_term_id']
+        print('Could not find url for sample ontology %s' % biosample['biosample_term_id'])
 
     sample_attribute = {
         'sample_id' : biosample['accession'],
@@ -346,7 +369,7 @@ def add_SA_with_donor(sample_attribute, donor):
 def add_SA_cell_line(sample_attribute, biosample):
     if sample_attribute['biomaterial_type'] == 'Cell Line':
         sample_attribute['line'] = biosample['biosample_term_name']
-        sample_attribute['differenciate_stage'] = biosample['biosample_term_name']
+        sample_attribute['differentiation_stage'] = biosample['biosample_term_name']
         sample_attribute['sex'] = biosample['sex'].title()
 
         #Get lineage
@@ -357,7 +380,7 @@ def add_SA_cell_line(sample_attribute, biosample):
             if len(biosamples_associated_with_donor) > 0:
                 sample_attribute['lineage'] = biosamples_associated_with_donor[0]['biosample_term_name']
             else:
-                print 'No stem cell biosamples associated with donor %s' % donor_accession
+                print('No stem cell biosamples associated with donor %s' % donor_accession)
         else:
             sample_attribute['lineage'] = ''
 
@@ -369,15 +392,27 @@ def add_SA_primary_cell(sample_attribute, biosample):
 
 def add_SA_primary_tissue(sample_attribute, biosample):
     if sample_attribute['biomaterial_type'] == 'Primary Tissue':
-        sample_attribute['tissue_type'] = biosample['biosample_term_id']
+        sample_attribute['tissue_type'] = biosample['biosample_term_name']
 
 
-def create_experiment_attributes(experiment):
+def create_experiment_attributes(experiment, registry_id):
     return {
+        "reference_registry_id": registry_id,
         "assay_type": experiment['assay_term_name'],
         "experiment_ontology_uri": 'http://purl.obolibrary.org/obo/%s' % experiment['assay_term_id']
     }
 
+
+def create_analysis_attributes(experiment):
+    # No mapping exists between the expected attributes and portal data for now
+    analysis_attributes = {
+        "analysis_group": "",
+        "alignment_software": "",
+        "alignment_software_version": "",
+        "analysis_software": "...",
+        "analysis_software_version": ""
+    }
+    return analysis_attributes
 ############################# Get ENCODE data #############################
 # These functions get ENCODE data from the webservices.
 
@@ -389,9 +424,9 @@ def prep_query_url(url, assembly, taxon_id, limit='all'):
     queries['format'] = ['json']
     queries['assembly'] = [assembly]
     queries['replicates.library.biosample.donor.organism.taxon_id'] = [str(taxon_id)]
-    query = '&'.join(['&'.join([key + '=' + value for value in values]) for key, values in queries.iteritems()])
+    query = '&'.join(['&'.join([key + '=' + value for value in values]) for key, values in queries.items()])
     new_url = urlparse.urlunparse((parsed.scheme, parsed.netloc, parsed.path, parsed.params, query, parsed.fragment))
-    print new_url
+    print(new_url)
     return new_url
 
 
diff --git a/IHEC_json_converter/reference_epigenome_experiments.py b/IHEC_json_converter/reference_epigenome_experiments.py
new file mode 100644
index 0000000..8e94359
--- /dev/null
+++ b/IHEC_json_converter/reference_epigenome_experiments.py
@@ -0,0 +1,30 @@
+import requests
+import json
+from general import *
+from rnaseq import *
+from bisulfite import *
+from chipseq import *
+
+
+
+API_ENDPOINT = "https://www.encodeproject.org"
+REFERENCE_EPIGENOME_COLLECTION = API_ENDPOINT + "/search/?type=ReferenceEpigenome&format=json&limit=all"
+
+def collect_experiments(assembly='hg19', taxon_id=9606):
+    dataset = dict()
+    response = requests.get(REFERENCE_EPIGENOME_COLLECTION)
+    
+    # Iterate over Reference Epigenomes
+    for reference_epigenome in response.json()['@graph']:
+        reference_epigenome_object = requests.get(API_ENDPOINT + reference_epigenome['@id']+'?format=json').json()
+        reference_registry_id = get_epirr_id(reference_epigenome_object)
+        
+        # Iterate over experiments in Reference Epigenomes
+        for experiment_obj in reference_epigenome_object['related_datasets']:
+            if 'assembly' in experiment_obj and experiment_obj['assembly'] and assembly in experiment_obj['assembly']:
+                addition = determine_addition(experiment_obj)
+                if addition:
+                    dataset.update(create_datasets(experiment_obj, reference_registry_id, addition))
+
+    data = convert_to_IHEC_format(dataset, assembly, taxon_id)
+    return data
\ No newline at end of file
diff --git a/IHEC_json_converter/rnaseq.py b/IHEC_json_converter/rnaseq.py
index fe7f964..45f4acc 100755
--- a/IHEC_json_converter/rnaseq.py
+++ b/IHEC_json_converter/rnaseq.py
@@ -1,52 +1,46 @@
 __author__ = 'kelley'
 
 import json
-from general import convert_to_IHEC_format, set_main_track, signal_mapping
 
 VERSION='1.6'
 
-def rna_seq_wrapper(assembly, taxon_id):
-    url = 'https://www.encodeproject.org/search/?type=experiment&assay_term_name=RNA-seq'
 
-    # Used to set is_main
-    track_hierarchy = {'signal_forward': ['plus strand signal of unique reads', 'plus strand signal of all reads',
+RNASEQ_TRACK_HIEARCHY = {'signal_forward': ['plus strand signal of unique reads', 'plus strand signal of all reads',
                                               'plus strand signal', 'raw plus strand signal'],
                            'signal_reverse': ['minus strand signal of unique reads', 'minus strand signal of all reads',
                                               'minus strand signal', 'raw minus strand signal'],
                            'signal': ['signal of unique reads', 'signal of all reads', 'signal', 'raw signal', 'splice junctions'],
                            'contigs': ['contigs']}
 
+
+def rna_seq_addition(experiment, json_object):
+
     size_range_to_experiment_type = {
         '>200': 'mRNA-seq',
         '<200': 'smRNA-seq'
     }
 
-    def dataset_additions_f(experiment, json_object):
-
-        #Set experiment_type
-        size_range = None
-        if 'size_range' in experiment['replicates'][0]['library']:
-            size_range = experiment['replicates'][0]['library']['size_range']
-
-        if size_range is None:
-            print 'Could not find size_range ' + experiment['accession']
-            json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
-            json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
-        elif size_range not in size_range_to_experiment_type:
-            print 'Size range not found: ' + experiment['replicates'][0]['library']['size_range']
-            json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
-            json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
-        else:
-            json_object['experiment_attributes']['experiment_type'] = size_range_to_experiment_type[size_range]
-            json_object['experiment_attributes']['assay_type'] = size_range_to_experiment_type[size_range]
-
-        return json_object
-
-    return convert_to_IHEC_format(url, assembly, taxon_id, track_hierarchy, dataset_additions_f)
-
-
-
-if __name__ == "__main__":
-    data = rna_seq_wrapper(assembly='hg19', taxon_id=9606)
-    with open('../output/RNAseq_v%s.json' % VERSION, 'w+') as outfile:
-        json.dump(data, outfile, indent=4)
\ No newline at end of file
+    #Set experiment_type
+    size_range = None
+    if 'size_range' in experiment['replicates'][0]['library']:
+        size_range = experiment['replicates'][0]['library']['size_range']
+
+    if size_range is None:
+        print('Could not find size_range ' + experiment['accession'])
+        json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
+        json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
+    elif size_range not in size_range_to_experiment_type:
+        print('Size range not found: ' + experiment['replicates'][0]['library']['size_range'])
+        json_object['experiment_attributes']['experiment_type'] = 'RNA-seq'
+        json_object['experiment_attributes']['assay_type'] = 'RNA-seq'
+    else:
+        json_object['experiment_attributes']['experiment_type'] = size_range_to_experiment_type[size_range]
+        json_object['experiment_attributes']['assay_type'] = size_range_to_experiment_type[size_range]
+
+    return json_object
+
+
+# if __name__ == "__main__":
+#     data = rna_seq_wrapper(assembly='hg19', taxon_id=9606)
+#     with open('../output/RNAseq_v%s.json' % VERSION, 'w+') as outfile:
+#         json.dump(data, outfile, indent=4)
\ No newline at end of file
diff --git a/README.md b/README.md
index 64c5b0d..b5bc220 100644
--- a/README.md
+++ b/README.md
@@ -5,11 +5,15 @@ These scripts fetch ENCODE metadata from the ENCODE portal, and output it in the
 
 #### Parameters
 
-* assembly: Assembly name (e.g. hg19, hg38, mm10)
-* taxon-id: Species taxonomy id (e.g. 9606 for human)
+* assembly: Assembly name (e.g. hg19, GRCh38, mm10)
+* taxon-id: Species taxonomy id (e.g. 9606 for human, 10090 for mouse)
 
 #### Example
 ```
 cd IHEC_json_converter
-python ./fetch_all_exp_jsons.py --assembly=hg19 --taxon-id=9606
+python3 ./fetch_all_exp_jsons.py --assembly=hg19 --taxon-id=9606
 ```
+
+### Credits
+
+Original development by ENCODE team, available here: https://github.com/kpaskov/PaskovEncodeScripts 
\ No newline at end of file
diff --git a/output/README.md b/output/README.md
new file mode 100644
index 0000000..5d0bba6
--- /dev/null
+++ b/output/README.md
@@ -0,0 +1 @@
+Placeholder for scripts output.
\ No newline at end of file