Differences

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--- mapping_rnaseq_data_to_your_genome [2024/10/24 14:09] – 75.152.217.185
+++ mapping_rnaseq_data_to_your_genome [2024/10/25 15:20] (current) – [What the script does] 134.190.144.194
@@ Line 114: / Line 114: @@
 -U forward_unpaired.fastq,reverse_unpaired.fastq
-#set the maximum (MX) and minimum (MN) mismatch penalties. Default: MX = 6, MN = 2.
+# set the maximum (MX) and minimum (MN) mismatch penalties. Default: MX = 6, MN = 2.
-#NOTE: you may have to increase this to get the optimal mapping of a read across an intron! I have noticed this is not always the case with the default penalty settings, so it is good to check -KW
+# NOTE: you may have to increase this to get the optimal mapping of a read across an intron!
+# I have noticed this is not always the case with the default penalty settings,
+# so it is good to check -Kelsey Williamson
 --mp MX,MN
-#set the penalty for non-canonical splice sites (non-GT/AG) - default is 12
+# set the penalty for non-canonical splice sites (non-GT/AG) - default is 12
+# so if your genome uses non-canonical splice sites, you want to set this to 0
 --pen-noncansplice <int>
 </code>