Take GSE105312 as example, anyone knows how to creat these two files? what's the different between them? I know they are from ENCODE Chip-seq assay.
Thanks.
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE105312
GSE105312_ENCFF580LHX_optimal_idr_thresholded_peaks_hg19.bed.gz GSE105312_ENCFF449YRH_conservative_idr_thresholded_peaks_hg19.bed.gz
Okay. Maybe I found the answers:
Final peak calls (bed and bigBed format) are the set of peak calls that pass IDR at a threshold of 2%. The conservative set are peaks derived from IDR analysis of biological replicates, whereas the optimal set are the largest set of peaks derived from IDR analysis of biological replicates and pseudoreplicates. Pseudoreplicates are peak sets called on half of the pooled reads, chosen at random without replacement
more details can check here:
https://www.encodeproject.org/chip-seq/transcription_factor/
0 answers
No answers yet.
Log in to answer this question.
-
Fixed peak width in ENCODE TFs ChIP-seq
written by DavideBrex •
-
Understanding Chip-seq data (ENCODE and other resources)
written by r.kalampaliki •
-
Question about ENCODE ATAC-seq bed file, bed narrowPeak vs bed idr_ranked_peak
written by yanweng •
-
Combining the original replicates and pseudo-replicates for differential binding analysis?
written by maisarasora •
-
Can we compare peaks of different transcription factors when they were obtained by different criter…
written by salamandra
-
Does IDR (irreproducible discovery rate) higher mean less 'reproducible' or vice versa?
written by sckinta
-
FAIRE-seq - actively maintained peak-callers
written by boczniak767
-
ChIP-Seq: Calling peaks with replicates
written by dariober
-
Apply Idr On List Of Read Counts
written by 14134125465346445
-
Irreproducible Discovery Rate
written by Dataminer
