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CRUNCH - A completely automated pipe-line for ChIP-seq data analysis, starting from raw sequencing reads, through quality filtering, read mapping, fragment size estimation, peak calling, peak annotation and comprehensive regulatory motif analysis. It runs with data from human (hg19), mouse (mm9) or drosophila (dm3).

Crunch: Completely Automated Analysis of ChIP-seq Data.
Severin Berger, Saeed Omidi, Mikhail Pachkov, Phil Arnold, Nicholas Kelley, Silvia Salatino, Erik van Nimwegen
Biorxiv, 2016

To analyse your data with CRUNCH, you only need to upload raw sequencing reads. The preferred format is FASTQ, but also FASTA format and a weighted BED format are allowed. Select the files you want to upload by clicking the 'Foreground files' and 'Background files' buttons for foreground (a.k.a. immunprecipitation, IP) and background (a.k.a. input, control or whole cell extract) files, respectively. You may select multiple files for both fore- and background and you may select uncompressed files, but we encourage users to upload gzip-compressed files (e.g. .fastq.gz). For human data you may omit the background files and only upload foreground files, although we advise to include the corresponding background files if available - for mouse and drosophila it is even mandatory.

Additionally, you may specify your email address so that we can notify you when your analysis is ready as well as a project name.

Although usually not necessary, the user may adjust advanced options:

Click 'Start upload' to upload your data and start the analysis. Now you are done.

Weighted BED format is 6-column BED format, where the 5th column of each line contains a weight which represents the number of reads that mapped to that position divided by the total number of positions this read was reported to map to.