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--- mapping_rnaseq_data_to_your_genome [2024/02/27 11:14] – [The perun shell script] 134.190.232.164
+++ mapping_rnaseq_data_to_your_genome [2024/10/25 15:20] (current) – [What the script does] 134.190.144.194
@@ Line 1: / Line 1: @@
 ====== Mapping RNAseq data to your genome ======
-Initially written by I don't know who. Updated by Joran Martijn, December 2023
+Initially written by I don't know who. Updated by Joran Martijn, December 2023. (Minor update, KW, Oct 2024)
@@ Line 113: / Line 113: @@
 # indicate one or more files containing unpaired reads
 -U forward_unpaired.fastq,reverse_unpaired.fastq
+# 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 -Kelsey Williamson
+--mp MX,MN
+# 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>