diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample
index 315525bc6183..0e026b5a7b0a 100644
--- a/lib/galaxy/config/sample/datatypes_conf.xml.sample
+++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample
@@ -114,7 +114,11 @@
     <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>
     <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="false"/>
     <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="false"/>
-    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>
+    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true">
+        <upload_warning>
+          SOLID Color-Space sequence data is a rare data type. Consider selecting fasta instead.
+        </upload_warning>
+    </datatype>
     <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
     <datatype extension="gz" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
@@ -148,6 +152,9 @@
     </datatype>
     <datatype extension="fastqsolexa" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="Solexa variant of the FASTQ format: solexa+64" description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+      <upload_warning>
+        Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
     </datatype>
     <datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true" description="sequence in in color space phred scored quality values 0:93 represented by ASCII 33:126">
       <upload_warning>
@@ -157,6 +164,9 @@
     </datatype>
     <datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true" description="Sanger variant of the FASTQ format: phred+64">
       <converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
+      <upload_warning>
+        Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
+      </upload_warning>
     </datatype>
     <datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
     <datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>