mapping_rnaseq_data_to_your_genome
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| mapping_rnaseq_data_to_your_genome [2024/10/25 10:48] – 134.190.144.194 | mapping_rnaseq_data_to_your_genome [2024/10/25 15:20] (current) – [What the script does] 134.190.144.194 | ||
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| # NOTE: you may have to increase this to get the optimal mapping of a read across an intron! | # 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, | # I have noticed this is not always the case with the default penalty settings, | ||
| - | # so it is good to check -KW | + | # so it is good to check -Kelsey Williamson |
| --mp MX,MN | --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> | --pen-noncansplice <int> | ||
| </ | </ | ||
mapping_rnaseq_data_to_your_genome.1729864109.txt.gz · Last modified: by 134.190.144.194