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YeoLab / skipper

Skip the peaks and expose RNA-binding in CLIP data
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Some misleading in Skipper_config.py #27

Closed Lindky closed 5 months ago

Lindky commented 5 months ago

I'm looking for clarification on the Skipper config file. Some terms really confused me.

Does the "STAR_DIR" refer to the STAR index folder?

Could you provide an example for the "REPEAT_TABLE"? I downloaded the coordinates of the repetitive element from the whole genome from the USCD genome browser with the repeatMasker format. However, I got an error that says the output file for the REPEAT_bed is missing. I'm wondering whether the format of my REPEAT_TABLE is correct.

byee4 commented 5 months ago

Does the "STAR_DIR" refer to the STAR index folder?

Yes that's correct

Could you provide an example for the "REPEAT_TABLE"? I downloaded the coordinates of the repetitive element from the whole genome from the USCD genome browser with the repeatMasker format. However, I got an error that says the output file for the REPEAT_bed is missing. I'm wondering whether the format of my REPEAT_TABLE is correct.

Here is an example of a repeat table: https://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz

The REPEAT_BED param should be a valid path but does not need to exist, as the pipeline will attempt to create this file from REPEAT_TABLE: https://github.com/YeoLab/skipper/blob/55bf887551af44a50f316cd39db48d330876cca7/Skipper.py#L383

Lindky commented 5 months ago

Thanks! It can now successfully run on my samples.