Differences

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--- mapping_rnaseq_data_to_your_genome [2024/10/24 14:05] – 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 113: / Line 113: @@
 # indicate one or more files containing unpaired reads
 -U forward_unpaired.fastq,reverse_unpaired.fastq
-</code>
-#set the penalty for non-canonical splice sites (non-GT/AG) - default is 12
+# 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>
 Note that in this script, the hisat2 output is directly fed into ''samtools sort'' which then generates a sorted BAM file immediately. The formation of a SAM file is thus skipped. This is beneficial because it reduces computation time, and the number of samtools commands to run. A SAM file is essentially unnecessary once you have the BAM file anyway. However, if you still wish to generate the SAM file, you can remove the pipe-into-samtools line and replace it with another option for hisat2: ''-S <output.sam>''