diff --git a/client/src/components/Collections/PairedListCollectionCreator.test.js b/client/src/components/Collections/PairedListCollectionCreator.test.js
index 0870092906d..ce54a281bd0 100644
--- a/client/src/components/Collections/PairedListCollectionCreator.test.js
+++ b/client/src/components/Collections/PairedListCollectionCreator.test.js
@@ -102,4 +102,39 @@ describe("PairedListCollectionCreator", () => {
         const pairname = wrapper.find("span.pair-name");
         expect(pairname.text()).toBe("UII_moo_1");
     });
+
+    it("autopairs correctly when filters are typed in", async () => {
+        wrapper = mount(PairedListCollectionCreator, {
+            propsData: {
+                initialElements: DATA._4,
+                creationFn: () => {
+                    return;
+                },
+                oncreate: () => {
+                    return;
+                },
+                oncancel: () => {
+                    return;
+                },
+                hideSourceItems: false,
+            },
+        });
+        await wrapper.vm.$nextTick();
+        //change filter to _R1/_R2
+        wrapper.find("div.forward-unpaired-filter > input").setValue("_R1");
+        await wrapper.vm.$nextTick();
+        wrapper.find("div.reverse-unpaired-filter > input").setValue("_R2");
+        await wrapper.vm.$nextTick();
+        //assert forward filter
+        const forwardFilter = wrapper.find("div.forward-unpaired-filter > input").element.value;
+        expect(forwardFilter).toBe("_R1");
+        //assert reverse filter
+        const reverseFilter = wrapper.find("div.reverse-unpaired-filter > input").element.value;
+        expect(reverseFilter).toBe("_R2");
+        // click Autopair
+        wrapper.find("a.autopair-link").trigger("click");
+        await wrapper.vm.$nextTick();
+        //assert all pairs matched
+        expect(wrapper.findAll("li.dataset unpaired").length == 0).toBeTruthy();
+    });
 });
diff --git a/client/src/components/Collections/PairedListCollectionCreator.vue b/client/src/components/Collections/PairedListCollectionCreator.vue
index 1e0175c7061..5bd7d66d3af 100644
--- a/client/src/components/Collections/PairedListCollectionCreator.vue
+++ b/client/src/components/Collections/PairedListCollectionCreator.vue
@@ -437,7 +437,10 @@ export default {
     mixins: [mixin],
     created() {
         this.strategy = this.autopairLCS;
-        this.filters = this.commonFilters[this.filters] || this.commonFilters[this.DEFAULT_FILTERS];
+        //TODO convert to Fwd/Rev
+        // Setup inital filters and shallow copy the items
+        this.forwardFilter = this.commonFilters[this.DEFAULT_FILTERS][0];
+        this.reverseFilter = this.commonFilters[this.DEFAULT_FILTERS][1];
         this._elementsSetUp();
     },
     components: {
@@ -462,15 +465,15 @@ export default {
                 dot12s: [".1.fastq", ".2.fastq"],
             },
             DEFAULT_FILTERS: "illumina",
-            filters: this.DEFAULT_FILTERS,
+            forwardFilter: "",
+            reverseFilter: "",
             automaticallyPair: true,
             initialPairsPossible: true,
             matchPercentage: 0.99,
             twoPassAutoPairing: true,
             removeExtensions: true,
             workingElements: [],
-            forwardFilter: "",
-            reverseFilter: "",
+
             selectedForwardElement: null,
             selectedReverseElement: null,
             /** autopair by exact match */
@@ -837,7 +840,7 @@ export default {
             var _regexps = [];
             function getRegExps() {
                 if (!_regexps.length) {
-                    _regexps = [new RegExp(this.filters[0]), new RegExp(this.filters[1])];
+                    _regexps = [new RegExp(this.forwardFilter), new RegExp(this.reverseFilter)];
                 }
                 return _regexps;
             }
@@ -925,8 +928,8 @@ export default {
             };
         },
         changeFilters: function (filter) {
-            this.filters[0] = this.forwardFilter = this.commonFilters[filter][0];
-            this.filters[1] = this.reverseFilter = this.commonFilters[filter][1];
+            this.forwardFilter = this.commonFilters[filter][0];
+            this.reverseFilter = this.commonFilters[filter][1];
         },
         clickedCreate: function (collectionName) {
             this.checkForDuplicates();
@@ -946,7 +949,6 @@ export default {
             this.pairedElements.forEach((pair) => {
                 if (Object.prototype.hasOwnProperty.call(existingPairNames, pair.name)) {
                     valid = false;
-                    console.log("found a dupe");
                     this.duplicatePairNames.push(pair.name);
                 }
                 existingPairNames[pair.name] = true;
diff --git a/client/tests/qunit/test-data/paired-collection-creator.data.js b/client/tests/qunit/test-data/paired-collection-creator.data.js
index 02a199980d5..a6c3c954568 100644
--- a/client/tests/qunit/test-data/paired-collection-creator.data.js
+++ b/client/tests/qunit/test-data/paired-collection-creator.data.js
@@ -28,6 +28,15 @@ var datasets3 = [
     {name: "UII_moo_1.2.fastq", state: STATES.OK}
 ]
 
+var datasets4= [
+    { name: "SET1-01_R1.fastq", state: STATES.OK },
+    { name: "SET1-01_R2.fastq", state: STATES.OK },
+    { name: "SET1-02_R1.fastq", state: STATES.OK },
+    { name: "SET1-02_R2.fastq", state: STATES.OK },
+    { name: "SET1-03_R1.fastq", state: STATES.OK },
+    { name: "SET1-03_R2.fastq", state: STATES.OK },
+]
+
 var datasets1CreateRequestJSON = {
     type: "dataset_collection",
     collection_type: "list:paired",
@@ -161,5 +170,6 @@ export default {
     _1: datasets1,
     _1requestJSON: datasets1CreateRequestJSON,
     _2: datasets2,
-    _3: datasets3
+    _3: datasets3,
+    _4: datasets4
 };