Question: ENCODE Chip-seq Data Format
2
gravatar for Shicheng Guo
2.0 years ago by
Shicheng Guo8.1k
Shicheng Guo8.1k wrote:

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/

chip-seq encode • 1.2k views
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Shicheng Guo8.1k
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