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fl-yu / CUT-RUNTools-2.0

CUT&RUN and CUT&Tag data processing and analysis
MIT License
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paths in bulk-config.jason file #39

Closed thugib closed 2 years ago

thugib commented 2 years ago

I noteiced in your bulk-config.json file your entry for java was: "javabin": "/homes6/fulong/miniconda3/envs/dfci1/bin", Where did the dfci conda environment come from ? I do not have this environment. Where should my javabind be directed to ?

Also, the memebin path is "memebin": "/homes6/fulong/miniconda3/envs/py3/bin",
I have a python3env conda environment, so I used that instead of py3.

And finally, for the bowtie index and genome.fa files. My guess is that you can put them anywhere you want. Is that true, or is there a particular folder that the bowtie index and genome.fa files should go ?

"bt2idx": "/gcdata/gcproj/fulong/Data/Genomes/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index", "genome_sequence": "/gcdata/gcproj/fulong/Data/Genomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa",

fl-yu commented 2 years ago

Hi thugib! You need to replace the path with the real one in your environment. For example, you may search for javabin with the command which java.

Re genome.fa: Yes, you can put them anywhere but please make sure they can be found by CUT&RUNTools2.0 (replace the path with the real one you have). For your convenience please follow our installation instrument which includes how to download the reference genome with bowtie2 index together.