alexg9010
commented
3 years ago Hi frylhc,
I just quickly tested the impact of the step size on the memory footprint and it is having a huge influence on memory consumption. My advice would be to increase the step size and have less overlap between the windows, this should lower the memory usage.
Best, Alex
On 1. Nov 2021, at 14:04, frylhc @.***> wrote:
Dear Altuna and all, Got questions again. I've got 12 samples, 6 for control and 6 for treatment, respectively. When tiling the genome, I set window size as 1000bp and step size as 10bp. Before tiling, the CX reports produced by the Bismark pipeline was read by methRead function and stored as flat file database. The tiling process is memory-consuming, and thus limited internal memory of my computer prevent me from executing DMR analysis. I was wondering if methylKit got solutions to deal with such issues? Thanks.
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frylhc
Dear Altuna and all, Got questions again. I've got 12 samples, 6 for control and 6 for treatment, respectively. When tiling the genome, I set window size as 1000bp and step size as 10bp. Before tiling, the CX reports produced by the Bismark pipeline was read by methRead function and stored as flat file database. The tiling process is memory-consuming, and thus limited internal memory of my computer prevent me from executing DMR analysis. I was wondering if methylKit got solutions to deal with such issues? Thanks.