Sequence Error Filtering Pipeline for FFPE Samples


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Documentation for package ‘MicroSEC’ version 1.1.3

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exampleBAM An example BAM file.
exampleMutation An example mutation file.
exampleMutCall An example mutated read ID file.
fun_analysis Analyzing function.
fun_convert Mutation data file converter
fun_hairpin_check Hairpin-structure sequence check function
fun_hairpin_trimming Adapter sequence trimming function
fun_homology Homology check function.
fun_insert_length Insert length checker for BAM file
fun_load_bam BAM file loader
fun_load_chr_no Chromosome number loading function.
fun_load_genome Genome loading function.
fun_load_id Mutation-supporting read ID files loader
fun_load_mutation Mutation data file loader
fun_load_mutation_gz Mutation data file loader
fun_read_check Read check function.
fun_repeat_check Repeat check function.
fun_save Save function.
fun_save_gz Save function.
fun_setting Mutated position search function.
fun_summary Summarizing function.
fun_support Supporting length calculation function.
fun_zero Devide function without 0/0 errors
homology_searched An example sequence infromation file.
msec_analyzed An example mutation file.
msec_homology_searched An example mutation file.
msec_read_checked An example mutation file.
msec_summarized An example mutation file.
mut_depth_checked An example sequence infromation file.