Hi, I have a fastq file from a TF targeted ChIP-seq run, obtained from GEO here: https://www.ncbi.nlm.nih.gov/sra?term=SRX011616
I need to process this data and do peak-calling for some downstream stuff, and as I am using it in tandem with other data that the Encode project has already processed, I would like to use their pipeline for quality control, alignment and peak calling. I saw they have their pipeline in a GUI on DNAnexus and was planning on using that; however I noticed that all of their ChIP-seq pipelines need a control fastq file, which my experiment doesn't seem to have. I saw that there are several control chip-seq assays availible on Encode for my cell line (human h1) -- could I use one of these, and if so, how would I go about choosing one? Also, I noticed that there are several different ChIP-seq pipelines for transcription factors on encode - Unary control, unreplicated is I think what I want as I only have one run, but I wanted to double check.
Thanks so much for any help!