.singleSplitUMI4C {UMI4Cats} | R Documentation |
Split fastq files at a given restriction site.
.singleSplitUMI4C( fastq_file, res_enz, cut_pos, split_dir, min_flen = 20, numb_reads = 1e+09 )
fastq_file |
Fastq file path. |
res_enz |
Character containing the restriction enzyme sequence. |
cut_pos |
Numeric indicating the nucleotide position where restriction enzyme cuts (zero-based) (for example, for DpnII is 0). |
split_dir |
Directory where to save split files. |
min_flen |
Minimal fragment length to use for selecting the fragments. Default=20 |
numb_reads |
Number of lines from the FastQ file to load in each loop. If having memory size problems, change it to a smaller number. Default=1e9. |
Creates a compressed FASTQ file in wk_dir/split
named
basename(fastq)).fq.gz
, containing the split reads based on the
restriction enzyme used.