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Taiji-pipeline / Taiji

All-in-one analysis pipeline
https://taiji-pipeline.github.io/
BSD 3-Clause "New" or "Revised" License
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Efficient way to generate new PageRank for slightly altered input file #20

Closed cong-003 closed 3 years ago

cong-003 commented 3 years ago

Hi Kai,

When I ran Taiji, I came across an error "Create_Linkage(58c2..) Failed: No gene available for domain assignment!". I checked the atac peak files and found some samples have no peaks at all. So I deleted those samples from my input file and also tried to let Taiji read my new input by following commands:

> taiji delete RNA_Read_Input
> taiji delete ATAC_Read_Input
> taiji run --config human_embryonic_config_hic.yml --select Output_Ranks

But it didn't work, so could you help me out please? Do I need to rerun all the previous steps before that? Is there more efficient way to do this?

Thanks a lot!

kaizhang commented 3 years ago

This requires an in-depth understanding of the workflow. I will add command-line options to facilitate such operations in future.

kaizhang commented 3 years ago

Added a new flag --delete-smart which may help in such situations. Example usage:

taiji delete RNA_Read_Input --delete-smart
taiji delete ATAC_Read_Input --delete-smart
taiji run --config human_embryonic_config_hic.yml --select Output_Ranks

Only steps that need an update will be rerun. This new feature will be incorporated in the next stable release. Close this issue for now.

cong-003 commented 3 years ago

Thanks, Kai!