Description Usage Arguments Details Value Author(s)
Sorts read pairs into three categories: flanking, facing, and fully repetitive.
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con |
database connection |
table_name |
name of table in database |
input_file |
inner_mate_range.tsv file (make sure chr names are compatible with your database) |
imd_dist |
.insert_length_dist file (i.e. the inner mate distance distribution file for the sample) |
upper_limit |
values between 0 and 1 will be used to set prob in quantile() and then used to calculate the maximum allowed distance from the repeat. Values greater than 1 will be applied as the maximum. Read pairs whose ends are farther from the repeat than the value set by this parameter will be not be used. [default= 0.95] |
margin |
minimum bp a read must be anchored outside the repeat [default= read_length/4] |
read_length |
read length |
min_repeat_length |
minimum repeat length in reference genome [default= 12] |
output_dir |
output directory to write results [default= "."] |
append_chr |
appends "chr" to chromosome names of inner_mate_ranges file if TRUE [default= TRUE] |
overwrite |
should output files be overwritten? [default= TRUE] |
margin |
maximum bp overlap between each read and a given repeat repeat [default= read_length/2] |
Description of output files: flanking: read pair completely flank the repeat or are anchored outside the repeat (minimum = margin) facing: one read flanks or is anchored outside the repeat (minimum = margin) while its pair aligned inside the repeat (or didn't meet minimum anchor requirements) fully_repetitive: both reads in pair aligned inside the repeat (or didn't meet minimum anchor requirements)
_flanking, _facing, and _fully_repetitive .tsv files
Adam Struck
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