How to analyze ChIP-seq with pipline?

Question

[solarchan7]

Hello, I am new to bioinformatics and i am trying to analyze/filter out nucleotide from a .fq file, I found this pipline (https://www.encodeproject.org/chip-seq/transcription_factor/) but how can i use it?Is it like r/python? Thank you :)

Answer 1

[dsull]

There are instructions here: https://github.com/ENCODE-DCC/chip-seq-pipeline2

[solarchan7]

but mine is a .fq file rather than a JSON file?

[dsull]

Per the instructions: "An input JSON file specifies all the input parameters and files that are necessary for successfully running this pipeline. This includes a specification of the path to the genome reference files and the raw data fastq file. Please make sure to specify absolute paths rather than relative paths in your input JSON files."

Aka you have to specify the .fq files in the JSON file.

[solarchan7]

okay thanks! I'll give it a try again!

[luckysardar171]

Can you please show some example how to run it I am new to chip_seq little bit confused how to run this code