Dear community,
I am new to bioinformatics and would greatly appreciate your advice.
I am currently working on integrating ChIP-seq data into the nf-core/chipseq pipeline and am specifically looking for H3K27me3 data in H9 cells. While I have found relevant datasets on the ENCODE database, I also require input data for the workflow.
In my search, I came across the following dataset: https://www.ncbi.nlm.nih.gov/sra?term=SRX2636164. This dataset contains three sequences (SRRs), and I am unsure which one to use for my analysis. From what I understand, these may represent technical replicates, but I am puzzled by the significant differences in their sizes.
Could anyone provide insights into why such size differences might occur and which sequence(s) would be most appropriate for my analysis?
Thank you!
These are not really technical replicates if they simply re-sequenced the same library three times. Resequencing multiplexed libraries on different lanes and flow cells is common and the variation in data signal is minimal.