Update FAQ.md

smithlabcode · Nov 22, 2015 · cfbcca3 · cfbcca3
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 ## Frequently Asked Questions ##
 
 1. When does WALT get much lower mapping rate (mapping effiency) compared to other bisulfite mappers?
-	By default, WALT ignores reads shorter than 39. If you get lower mapping rate, please go to mapstats file and check the percentage of reads that are shorter than 39. If a large portion of reads are shorter than 39, I suggest you use WALT seed pattern 7.
-	(1)	Open walt/src/walt/Makefile, modify “-D SEEDPATTERN3" to " -D SEEDPATTERN7"
-	(2)	rebuild the program using make all, make install
-	(3)	rebuild your index using the new makedb command
-	(4)	mapping reads using the new walt command
+
+	By default, WALT ignores reads shorter than 39. If you get lower mapping rate, please go to mapstats file and check the 			percentage of reads that are shorter than 39. If a large portion of reads are shorter than 39, I suggest you use WALT seed 	pattern 7.
+
+	(1) Open walt/src/walt/Makefile, modify “-D SEEDPATTERN3" to " -D SEEDPATTERN7"
+
+	(2) rebuild the program using make all, make install
+
+	(3) rebuild your index using the new makedb command
+
+	(4) mapping reads using the new walt command
+
+