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rfael0cm / RTIGER

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Tiling Distance #11

Open ngorringe opened 9 months ago

ngorringe commented 9 months ago

Hello there,

I am trying to run RTIGER on my data set and keep getting this error:

Error in RTIGER(expDesign = expDesign, outputdir = "PATH", : Your tiling distance is larger than some of your chromosomes. Reduce the tiling parameter.

Any help is greatly appreciated! Thank you in advance :)

NJ

rfael0cm commented 8 months ago

Dear NJ, thank you very much for getting in contact with us regarding this problem. This error arise when any of your chromosome lengths (seqlengths parameter in RTIGER) is shorter than the tiles parameter. tiles is a priory segmentation used by our algorithm to estimate the number of COs. The default value is 4e5 what it is intentionally short. Is any of your chromosomes shorter than this? If so, modify tiles such that tiles = shortest_chromosome/2.

Let me know if this fixes the problem and if there is something else I can help you with. Best, Rafael

ngorringe commented 8 months ago

Hiya Rafael,

Thank you for getting back to me! None of my chromosomes are shorter than 4e5 - the shortest is 21e7 but coverage differs quite a bit between replicates. I will try adding in the tiles argument.

Best, NJ