Understanding SICER2 Outputs

This page is to help you understand what the output files of SICER2 are. The number of files that SICER2 generates depends on whether or not control library is used and whether or not --significant_reads flag was set.

SICER Outputs

Base Outputs

  • treatment_file-W200-G600.scoreisland: this file is delineation of significant islands controlled by E- value of 1000. It is in “chrom start end score” format. "W200" and "G600" each respectively represents the window size and gap size parameters.

  • treatment_file-W200-normalized.wig: wig file that can be used to visualize the windows generated by SICER2. Read count is normalized by library size per million. "W200" reprsents the window sie parameter.

Additional outputs when control library is used

  • treatment_file-W200-G600-islands-summary: summary of all candidate islands with their statistical significance. It has the following format: chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold.
  • treatment_file-W200-G600-FDR0.01-island.bed: delineation of significant islands filtered by false discovery rate (FDR). It has the following format: chrom, start, end, read-count. "FDR0.01" represents the FDR parameter.

Additional outputs when --significant_reads flag is set

  • treatment_file-W200-G600-FDR0.01-islandfiltered.bed: library of reads in significant islands determined by SICER. Note that reads have been processed for redundancy.

  • treatment_1-W200-G600-FDR0.01-islandfiltered-normalized.wig: wig file of the reads from above file (i.e. island-filtered reads). This file can be uploaded to the UCSC genome browser and be compared with the track for treatment_file-W200-normalized.wig for visual examination of parameter choices and SICER performance.


The outputs of RECOGNICER are identical to SICER outputs except for one file. Instead of treatment_file-W200-G600.scoreisland file, treatment_file-W200-G600.cgisland is generated. Also, "G600" part is dropped from the name of the files since gap size is not a parameter for RECOGNICER.

  • treatment_file-W200.cgisland: like the *.scoreisland file produced by SICER, cgisland file is delineation of significant islands discovered using RECOGNICER algorithm. It is in “chrom start end score” format. "W200" represents the window size.