.singleCounterUMI4C {UMI4Cats} | R Documentation |
Count UMIs for a given bam file.
.singleCounterUMI4C( filtered_bam_R1, filtered_bam_R2, digested_genome_gr, pos_viewpoint, res_enz, count_dir, filter_bp = 1e+07 )
filtered_bam_R1 |
R1 bam file. |
filtered_bam_R2 |
R2 bam file. |
digested_genome_gr |
GRanges object containing the coordinates for the digested genome. |
pos_viewpoint |
Vector consist of chromosome, start and end position of the viewpoint. |
res_enz |
Character containing the restriction enzyme sequence. |
count_dir |
Counter directory. |
filter_bp |
Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6 |
Creates a tab-delimited file in wk_dir/count
named
"basename(fastq) _counts.tsv
", containing the
coordinates for the viewpoint fragment, contact fragment and the number of
UMIs detected in the ligation.