This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
I am performing peak calling with various tools (macs2, PeakSeq, CSAR, SPP). In order to perform peak calling in macs2 without model building (--nomodel and --ext size) we need to provide an estimated fragment length. Since run_spp.R provides the information of the estimated fragment length, I performed the analysis.
It is observed that the peak quality of the chip bam file is "2" and strand shift value with maximum correlation at "-5". I couldn't understand the result. The next two-strand shift values are 190 and 215. Can you or anyone help me to understand the result?
I posted a similar question on "[biostar]" but I didn't get any response.
Hello,
I am performing peak calling with various tools (macs2, PeakSeq, CSAR, SPP). In order to perform peak calling in macs2 without model building (--nomodel and --ext size) we need to provide an estimated fragment length. Since run_spp.R provides the information of the estimated fragment length, I performed the analysis.
It is observed that the peak quality of the chip bam file is "2" and strand shift value with maximum correlation at "-5". I couldn't understand the result. The next two-strand shift values are 190 and 215. Can you or anyone help me to understand the result?
I posted a similar question on "[biostar]" but I didn't get any response.
Thank you