This mode is used to convert sequences to mimick bisulfite conversion of unmethylated cytosines. It is implemented by
edu.cornell.med.icb.goby.modes.BisulfiteConversionMode.java. The mode converts C bases to T in primary and pair sequences. It can therefore be used to convert reference sequences (to index them and map bisulfite treated reads), or to create bisulfite treated reads in silico for simulation experiments. Since Goby 1.8.
Mode Parameters
The following options are available in this mode
| Flag | Arguments | Required | Description |
|---|---|---|---|
(-i|--input) | input | yes | Name of the compact reads input file. |
(-o|--output) | output | yes | Name of the compact reads output file. Sequences will be written to this output after bisulfite conversion (C->T). |
(-n|--sequence-per-chunk) | sequence-per-chunk | no | The number of sequences that will be written in each compressed chunk. Default is suitable for very many short sequences. Reduce to a few sequences per chunk if each sequence is very large. Default value: 10000 |
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