View source: R/copy_separate.R
copy_separate | R Documentation |
Separates two or more gene copies from short-read Next-Generation Sequencing data into a small number of overlapping DNA sequences.
copy_separate( filename, copy_number, read_length, overlap = 225, rare_read = 10, verbose = 1 )
filename |
A fasta file contains thousands of short reads that have been mapped to a reference. The reference and reads that are not directly mapped to the reference need to be removed after mapping. |
copy_number |
An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies in the input file. |
read_length |
An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length >=250bp. |
overlap |
An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. Default 225. |
rare_read |
A positive integer. During clustering analyses, clusters with less than this number of reads will be ignored. Default 10. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
A fasta alignment of a small number of overlapping DNA sequences covering the entire length of the target gene. Gene copies can be assembled by reordering the alignment manually or use the function "copy_assemble".
## Not run: copy_separate("inst/extdata/toydata.fasta",2,300,225,10,1) ## End(Not run)
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