HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup

The hicup2juicer script converts HiCUP BAM/SAM files to a format compatible with Juicer and JuiceBox( https://github.com/aidenlab/juicer ). Outputfiles generated by this script may be converted to Juicer ".hic" files using the "pre" command as described at: https://github.com/aidenlab/juicer/wiki/Pre

The script does not use restriction site coordinates when generating output.

FUNCTION

HiCUP generates SAM/BAM files of mapped, filtered paired-end reads constituting the sequenced valid Hi-C di-tags. These may then be analysed by a variety of specialised tools, but before this is possible the datasets will need parsing into an appropriate format.

The hicup2juicer script converts HiCUP BAM/SAM files to a tab-delimited format comprising 7 columns, with read pairs on the same line:

<readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse) chr = chromosome (must be a chromosome in the genome) pos = position frag = restriction site fragment mapq = mapping quality score

Column1: Readpair index number (starting at 1) Column2: forward read strand (0 = positive strand, 1 = negative strand) Column3: forward read chromosome name Column4: forward read position Column5: forward read fragment id (set to the dummy value 0) Column6: reverse read strand (0 = positive strand, 1 = negative strand) Column7: reverse read chromosome name Column8: reverse read position Column9: reverse read fragment id (set to the dummy value 1) Column10: forward read MAPQ score Column11: reverse read MAPQ score

COMMAND LINE OPTIONS

Full instructions on running the pipeline can be found at: www.bioinformatics.babraham.ac.uk/projects/hicup

Steven Wingett, Babraham Institute, Cambridge, UK