Understanding the output files

racoon_clip produces a variety of files during the different steps of the workflow. The files you will likely want to use downstream of racoon_clip are:

racoon_clip crosslink produces:

  • a summary of the performed steps called Report.html.

  • the sample-wise whole aligned reads after duplicate removal in bam format. You can find them in the folder results/aligned/<sample_name>.Aligned.sortedByCoord.out.duprm.bam together with the corresponding bam.bai files.

  • the group-wise whole aligned reads after duplicate removal in bam format. There will be one bam file for each group you specified in the group.txt file. If no group is specified, you get a file called all.bam where all samples are merged. They are located in the results/bam_merged/ folder.

  • the sample-wise single-nucleotide crosslink files in bw format.: The files are split up into the plus and minus strands. They are located at results/bw/<sample_name>sortedByCoord.out.duprm.minus.bw and results/bw/<sample_name>sortedByCoord.out.duprm.plus.bw.

  • the group-wise single-nucleotide crosslink files in bw format.: The files are split up into the plus and minus strands. They are located at results/bw_merged/<sample_name>sortedByCoord.out.duprm.minus.bw and results/bw_merged/<sample_name>sortedByCoord.out.duprm.plus.bw.

racoon_clip peaks produces:

  • all of the files above

  • the called binding peaks in bed format. Peak calling is performed on the merged groups. The peaks are located at results/peaks/<group_name>.bed