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Chrom3D / preprocess_scripts

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needing documantation #1

Open AhlemBoudell opened 4 years ago

AhlemBoudell commented 4 years ago

Hi all,

Thanks for posting your work for all of us to use! I am new to this field and i downloaded the Chrom3D src and used it to run the test data and worked fine. Now i wanted to use it for some row HiC data that i have but couldnt manage to find proper documentation on how to convert the fastq files into gtrack files. Can you please help me with which script to do what ?

Ahlem

jonnings commented 4 years ago

Hi! Have you seen the pipeline here? If you first use HiC-Pro for fastq-mapping and processing, then you should be able to modify this pipeline to generate the GTrack file.

AhlemBoudell commented 4 years ago

Hi,

Thanks for your reply! I was avoiding any use of HiC-pro as for some reason it kept throwing errors when i used it before and am not sure if the version installed in our cluster is faulty or i did something so wrong. I tried contacting the HiC-pro people to help with debugging and their fixes didnt work. I am using now another pipeline called HiCstuff to generate the contact maps from the fastq files, do you have another suggestion other than HiC-pro to do the mapping and the preprocessing?