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!
•
written
by
mark.pekarsky •
0 answers
No answers yet.
Log in to answer this question.
-
How to perform cross-species integration?
written by Shankar112 •
-
When there are multiple runs within a single experiment (in RNA-seq analysis)
written by wyt1995 •
-
Per base sequence content failed in fastQC
written by yliueagle
-
Do we have Alt Aware peak calling tools also?
written by rohitsatyam102
-
Exploring H3K27me3 loss in cancer
written by Researcher
-
Determining Significance of Enrichment Analysis Within Clustering to Compare Clustering Methods
written by adavi140 •
-
linc noncoding RNA from chIPseq
written by kanwarjag
-
macs2 param for H3K27me3 and H3K9me3
written by chipseq33 •
-
apply cufflinks to ENCODE RNA-Seq data
written by liu4gre
-
Chipseq Data On Prostate Cancer
written by Bioinfosm
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.