diff --git a/src/cli/BAM_Format_Converter/BAMtoBEDCLI.java b/src/cli/BAM_Format_Converter/BAMtoBEDCLI.java
index 769d34b66..60937985e 100644
--- a/src/cli/BAM_Format_Converter/BAMtoBEDCLI.java
+++ b/src/cli/BAM_Format_Converter/BAMtoBEDCLI.java
@@ -86,6 +86,8 @@ private String validateInput() throws IOException {
 		else if(readType.midpoint)	{ STRAND=3; }
 		else if(readType.fragment)	{ STRAND=4; }
 		else						{ STRAND=0; }
+		// set PE defaults
+		if(STRAND==3 || STRAND==4) { matePair=true; }
 		
 		//check inputs exist
 		if(!bamFile.exists()){
@@ -131,7 +133,7 @@ private String validateInput() throws IOException {
 		// validate insert sizes
 		if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
 		if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
-		if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
+		if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
 		// turn pair status boolean into int
 		PAIR = matePair ? 1 : 0;
 		
diff --git a/src/cli/BAM_Format_Converter/BAMtoGFFCLI.java b/src/cli/BAM_Format_Converter/BAMtoGFFCLI.java
index dfb7ada08..91fb0d958 100644
--- a/src/cli/BAM_Format_Converter/BAMtoGFFCLI.java
+++ b/src/cli/BAM_Format_Converter/BAMtoGFFCLI.java
@@ -86,6 +86,8 @@ private String validateInput() throws IOException {
 		else if(readType.midpoint)	{ STRAND=3; }
 		else if(readType.fragment)	{ STRAND=4; }
 		else						{ STRAND=0; }
+		// set PE defaults
+		if(STRAND==3 || STRAND==4) { matePair=true; }
 		
 		//check inputs exist
 		if(!bamFile.exists()){
@@ -131,7 +133,7 @@ private String validateInput() throws IOException {
 		// validate insert sizes
 		if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
 		if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
-		if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
+		if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
 		// turn pair status boolean into int
 		PAIR = matePair ? 1 : 0;
 		
diff --git a/src/cli/BAM_Format_Converter/BAMtobedGraphCLI.java b/src/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
index 26d885835..55b9a44b6 100644
--- a/src/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
+++ b/src/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
@@ -81,6 +81,8 @@ private String validateInput() throws IOException {
 		else if(readType.combined)	{ STRAND=2; }
 		else if(readType.midpoint)	{ STRAND=3; }
 		else						{ STRAND=0; }
+		// set PE defaults
+		if(STRAND==3) { matePair=true; }
 		
 		//check inputs exist
 		if(!bamFile.exists()){
@@ -119,7 +121,7 @@ private String validateInput() throws IOException {
 		// validate insert sizes
 		if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
 		if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
-		if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
+		if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
 		// turn pair status boolean into int
 		PAIR = matePair ? 1 : 0;
 		
diff --git a/src/cli/BAM_Format_Converter/BAMtoscIDXCLI.java b/src/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
index 4bf50d4c1..16c18c37a 100644
--- a/src/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
+++ b/src/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
@@ -83,6 +83,8 @@ private String validateInput() throws IOException {
 		else if(readType.combined)	{ STRAND=2; }
 		else if(readType.midpoint)	{ STRAND=3; }
 		else						{ STRAND=0; }
+		// set PE defaults
+		if(STRAND==3) { matePair=true; }
 		
 		//check inputs exist
 		if(!bamFile.exists()){
@@ -128,7 +130,7 @@ private String validateInput() throws IOException {
 		// validate insert sizes
 		if( MIN_INSERT<0 && MIN_INSERT!=-9999 ){ r += "MIN_INSERT must be a positive integer value: " + MIN_INSERT + "\n"; }
 		if( MAX_INSERT<0 && MAX_INSERT!=-9999 ){ r += "MAX_INSERT must be a positive integer value: " + MAX_INSERT + "\n"; }
-		if( MAX_INSERT<MIN_INSERT ){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
+		if( MAX_INSERT<MIN_INSERT && MIN_INSERT!=-9999 && MAX_INSERT!=-9999){ r += "MAX_INSERT must be larger/equal to MIN_INSERT: " + MIN_INSERT + "," + MAX_INSERT + "\n"; }
 		// turn pair status boolean into int
 		PAIR = matePair ? 1 : 0;
 		
diff --git a/src/cli/BAM_Manipulation/FilterforPIPseqCLI.java b/src/cli/BAM_Manipulation/FilterforPIPseqCLI.java
index 170fb7ea6..2beb8e465 100644
--- a/src/cli/BAM_Manipulation/FilterforPIPseqCLI.java
+++ b/src/cli/BAM_Manipulation/FilterforPIPseqCLI.java
@@ -107,7 +107,7 @@ private String validateInput() throws IOException {
 		}
 		
 		//check filter string is valid ATCG
-		Pattern seqPat = Pattern.compile("[ATCG]");
+		Pattern seqPat = Pattern.compile("[ATCG]+");
 		Matcher m = seqPat.matcher( filterString );
 		if( !m.matches() ){
 			r += "(!)Filter string must be formatted as a nucleotide sequence.\n" + filterString +
diff --git a/src/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java b/src/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
index b92d72af1..e4fa1d92a 100644
--- a/src/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
+++ b/src/cli/Coordinate_Manipulation/GFF_Manipulation/GFFtoBEDCLI.java
@@ -70,8 +70,8 @@ private String validateInput() throws IOException {
 		}else{
 			//check ext
 			try{
-				if(!"gff".equals(ExtensionFileFilter.getExtension(output))){
-					r += "(!)Use GFF extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".gff\n";
+				if(!"bed".equals(ExtensionFileFilter.getExtension(output))){
+					r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".bed\n";
 				}
 			} catch( NullPointerException e){ r += "(!)Output filename must have extension: use GFF extension for output filename. Try: " + output + ".gff\n"; }
 			//check directory
diff --git a/src/cli/Figure_Generation/CompositePlotCLI.java b/src/cli/Figure_Generation/CompositePlotCLI.java
index ace724c9c..643ff9b3a 100644
--- a/src/cli/Figure_Generation/CompositePlotCLI.java
+++ b/src/cli/Figure_Generation/CompositePlotCLI.java
@@ -104,7 +104,7 @@ public Integer call() throws Exception {
 		// Save Composite Plot
 		OutputStream OUT = new FileOutputStream(output);
 		ChartUtilities.writeChartAsPNG(OUT, chart, pixelWidth, pixelHeight);
-				
+		
 		System.err.println( "Image Generated." );
 		return(0);
 	}
@@ -140,8 +140,6 @@ private String validateInput() throws IOException {
 			}
 		}
 		
-		//set default title name
-		if(title!=null){ title = compositeData.getName(); }
 		//check pixel ranges are valid
 		if(pixelHeight<=0){ r += "(!)Cell height must be a positive integer value! check \"-y\" flag.\""; }
 		if(pixelWidth<=0) { r += "(!)Cell width must be a positive integer value! check \"-x\" flag.\""; }
diff --git a/src/cli/Read_Analysis/AggregateDataCLI.java b/src/cli/Read_Analysis/AggregateDataCLI.java
index 52365e74e..40fb9ce26 100644
--- a/src/cli/Read_Analysis/AggregateDataCLI.java
+++ b/src/cli/Read_Analysis/AggregateDataCLI.java
@@ -149,6 +149,10 @@ private String validateInput() throws IOException {
 		else if(aggr.max) { aggType = 5; }
 		else if(aggr.var) { aggType = 6; }
 		
+		//validate row&column start indexes
+		if(startROW<0){ r += "(!)Row start must not be less than zero\n"; }
+		if(startCOL<0){ r += "(!)Column start must not be less than zero\n"; }
+				
 		return(r);
 	}
 }
\ No newline at end of file
diff --git a/src/cli/Sequence_Analysis/SearchMotifCLI.java b/src/cli/Sequence_Analysis/SearchMotifCLI.java
index 67dfd3667..6757ac03f 100644
--- a/src/cli/Sequence_Analysis/SearchMotifCLI.java
+++ b/src/cli/Sequence_Analysis/SearchMotifCLI.java
@@ -6,6 +6,8 @@
 import picocli.CommandLine.Parameters;
 
 import java.util.concurrent.Callable;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import java.io.File;
 import java.io.IOException;
@@ -83,6 +85,14 @@ private String validateInput() throws IOException {
 			}
 		}
 		
+		//check filter string is valid ATCG
+		Pattern seqPat = Pattern.compile("[ATCG]+");
+		Matcher m = seqPat.matcher( motif );
+		if( !m.matches() ){
+			r += "(!)Motif string must be formatted as a nucleotide sequence.\n" + motif +
+				" is not a valid nucleotide sequence.\nExpected input string format: \"[ATCG]\"";
+		}
+		
 		//check mismatch value
 		if(ALLOWED_MISMATCH<0){ r += "(!)Please use a non-negative integer for allowed mismatches."; }
 		
diff --git a/src/scripts/BAM_Manipulation/FilterforPIPseq.java b/src/scripts/BAM_Manipulation/FilterforPIPseq.java
index 74544a25e..f011d965f 100644
--- a/src/scripts/BAM_Manipulation/FilterforPIPseq.java
+++ b/src/scripts/BAM_Manipulation/FilterforPIPseq.java
@@ -24,9 +24,9 @@ public class FilterforPIPseq {
 	File genome = null;
 	File output = null;
 	String SEQ = "";
-	
-	private PrintStream PS;
-	
+
+	private PrintStream PS = null;
+
 	public FilterforPIPseq(File in, File gen, File out, String s, PrintStream ps) {
 		bamFile = in;
 		genome = gen;
@@ -34,27 +34,28 @@ public FilterforPIPseq(File in, File gen, File out, String s, PrintStream ps) {
 		SEQ = s.toUpperCase();
 		PS = ps;
 	}
-	
+
 	public void run() throws IOException, InterruptedException {
 		IndexedFastaSequenceFile QUERY = new IndexedFastaSequenceFile(genome);
-		
+
 		IOUtil.assertFileIsReadable(bamFile);
 		IOUtil.assertFileIsWritable(output);
 		final SamReader reader = SamReaderFactory.makeDefault().open(bamFile);
 		reader.getFileHeader().setSortOrder(SAMFileHeader.SortOrder.coordinate);
 		final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, output);
-		
+
 		printBoth(bamFile.getName()); //output file name to textarea
-		
+
 		//Code to get individual chromosome stats
 		AbstractBAMFileIndex bai = (AbstractBAMFileIndex) reader.indexing().getIndex();
 		for (int z = 0; z < bai.getNumberOfReferences(); z++) {
 			SAMSequenceRecord seq = reader.getFileHeader().getSequence(z);
+
 			printBoth(seq.getSequenceName());
-					
+
 			CloseableIterator<SAMRecord> iter = reader.query(seq.getSequenceName(), 0, seq.getSequenceLength(), false);
 			while (iter.hasNext()) {
-				//Create the record object 
+				//Create the record object
 				SAMRecord sr = iter.next();
 				if(sr.getReadPairedFlag()) {
 					if(sr.getProperPairFlag() && sr.getFirstOfPairFlag()) {
@@ -70,7 +71,7 @@ public void run() throws IOException, InterruptedException {
 							}
 						}
 						//System.out.println(sr.getReadString() + "\t" + seq.getSequenceName() + "\t" + sr.getUnclippedStart() + "\t" + sr.getUnclippedEnd() + "\t" + sr.getReadNegativeStrandFlag() + "\t" + filter);
-						if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }							
+						if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }
 					}
 				} else {
 					String filter = "";
@@ -83,7 +84,7 @@ public void run() throws IOException, InterruptedException {
 						filter = FASTAUtilities.RevComplement(filter);
 					}
 					//System.out.println(sr.getReadString() + "\t" + seq.getSequenceName() + "\t" + sr.getUnclippedStart() + "\t" + sr.getUnclippedEnd() + "\t" + sr.getReadNegativeStrandFlag() + "\t" + filter);
-					if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }		
+					if(filter.toUpperCase().equals(SEQ)) { writer.addAlignment(sr); }
 				}
 			}
 			iter.close();
@@ -93,7 +94,7 @@ public void run() throws IOException, InterruptedException {
 		reader.close();
 		bai.close();
 	}
-	
+
 	private void printBoth(String message){
 		if(PS!=null){ PS.println(message); }
 		System.err.println(message);