Choosing the "right" sequence as an input control

Question

[mark.pekarsky]

Hello everyone, when I am looking for sequences for ChIPseq analysis, there are usually multiple links, for example, for the control sequences. https://www.encodeproject.org/experiments/ENCSR792GCH/ So which one should I choose?

Thanks a lot.

[ATpoint]

Why not using both? Check if it is technical replicates. If so merge the fastq files before alignment. If not, could be one control per biological replicates, then call peaks per sample against the respective control. Please in the future include a link to the dataset. I am hesitant to put effort finding the dataset as this is your duty to provide.