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pi-zz-a / CelFEER

Adaptation of CelFiE by Caggiano et al. (2021)
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Input File for CelFEER #1

Closed NichKu closed 2 years ago

NichKu commented 2 years ago

Great work! Are you also planning to upload a script to generate the input file for celfeer.py?

pi-zz-a commented 2 years ago

Hi @NichKu , thank you, I can definitely do that. I will get back to you!

pi-zz-a commented 2 years ago

@NichKu it is not entirely clear for me what you are asking for. Are you asking for the full pipeline from fastq files to read counts?

NichKu commented 2 years ago

Thanks for your response. If you can provide that it would be very helpful! If not, then I would just appreciate the code you used to create the file with the read methylation percentage in the 500bp windows from e.g. a bam file. The marker file you uploaded is only for chromosome 1. Would you mind providing the full marker file you used for the ALS cfDNA data (the one you used for intersecting with the cfDNA data)?

pi-zz-a commented 2 years ago

Hi @NichKu , I provided the complete file of ALS markers we found, and provided a guide on how to process read data, as well as some scripts, both of which you can find in scripts/data_processing. Unfortunately I don't have a streamlined workflow to provide you.

NichKu commented 2 years ago

Thanks a lot! It works, really appreciate it.