In GitLab by @magr0763 on Sep 28, 2018, 09:19
Currently, you can specify that the bedGraph provided for training contains information on both strands. However, there are a couple of bugs with this:
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In the help for arguments, it states that to do so, it's -strand both. This is incorrect -- in main_train.cpp, I determined it is "-strand ." (lines 71, 110&120 commented out currently, 127, 201). Lines 202-207 then print an error and instead default to training only using positive regions. We should remove this error and fix the argument
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FStitch by nature is strand specific, therefore training on just the positive reads is sufficient. As such, it would be useful if the user could provide a concatenated pos/neg strand bedGraph, however an error is not required, but rather a simple message saying positive strand only will be trained I think would suffice. There are a few options here, but this seems like it would be the easiest as long as it is well documented in the help and user guide
In GitLab by @magr0763 on Sep 28, 2018, 09:19
Currently, you can specify that the bedGraph provided for training contains information on both strands. However, there are a couple of bugs with this:
In the help for arguments, it states that to do so, it's -strand both. This is incorrect -- in main_train.cpp, I determined it is "-strand ." (lines 71, 110&120 commented out currently, 127, 201). Lines 202-207 then print an error and instead default to training only using positive regions. We should remove this error and fix the argument
FStitch by nature is strand specific, therefore training on just the positive reads is sufficient. As such, it would be useful if the user could provide a concatenated pos/neg strand bedGraph, however an error is not required, but rather a simple message saying positive strand only will be trained I think would suffice. There are a few options here, but this seems like it would be the easiest as long as it is well documented in the help and user guide