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BINDetect "ERROR IN REGION" #243
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Hi @liz-is, Is this still an issue? Technically TOBIAS should just count any regions without signal as 0, so I am not sure what is going on there. Can you share your version of TOBIAS and pyBigWig, e.g. with |
I don't have a solution yet, but I just realised that one of the bigwig files used as input here is suspiciously small and also can't be loaded by IGV, although the logs don't suggest any issues with its creation. So I suspect that is the issue. I'll delete that file and try to re-run. It would maybe be helpful if the logs printed the condition that was being processed to make it easier to identify if a particular file is causing a problem? Edit: forgot to include the versions, sorry, here they are:
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Hi @liz-is, Ah I see, yes I guess it is an error arising from reading a corrupt bigwig file, so hopefully it is solved by the recalculation of the .bw. But I totally agree as well, the error is not really helpful - I will improve on that for the next version! So I will just keep this issue open for reference to myself 👍 |
Hi, unfortunately after solving my issue with the ATACorrect step I'm running into a problem with BINDetect for the same data!
I get "ERROR IN REGION" for the first region in the bed file. I've previously used the same bed file for other conditions without issue. Looking at the code, I think the issue might be that there's no data in this region of the genome for one of the conditions. This is very plausible as I'm running TOBIAS on scATAC-seq data with aggregated data within different clusters as the different conditions.
Can you suggest a way I could pre-filter the regions to remove ones that don't have enough data in these clusters? There are definitely more regions with that give this same error - when running using multiple processes I see more instances of this error. Or would it be possible for TOBIAS to handle these a different way, e.g. by skipping and moving to the next region?
Here's the relevant part of the logs, please let me know if you need any more information!
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