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grenaud / gargammel

gargammel is an ancient DNA simulator
GNU General Public License v3.0
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fixed seed and add an annotation in the simulated read header #17

Closed chenjie2022 closed 2 years ago

chenjie2022 commented 2 years ago

Hi Gabriel,

Currently gargammel simulates datasets by randomly extracting reads from a genome. Would it be possible to (1) add an option to take fixed seed as input, so that for a genome we can generate different simulated datasets with different damage degrees (both for fragSim or deamSim), while for each of these generated datasets we have every read coming from exactly the same position on the reference genome? In other word, we can simulate different damage degrees on the same reads; and (2) add an annotation in the simulated read header to indicate that a (or mutiple) C>G or A>T damage was added?

grenaud commented 2 years ago

Hello! I have added the seed in fragSim, seems to work, I will add it in deamSim tomorrow :-)

grenaud commented 2 years ago

Hello! I have now added the seed to deamSim. For the type, it is relatively to infer, use the -name option and if you see a positive number ex: _DEAM:5 then it was a C to T, _DEAM:-5 was a G to A?

Let me know if you have any further requests :-)