CRUNCH

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/mm10), rat (rn6) or drosophila (dm3).

Crunch: Integrated processing and modeling of ChIP-seq data in terms of regulatory motifs
Severin M Berger, Mikhail Pachkov, Phil Arnold, Saeed Omidi, Nicholas Kelley, Silvia Salatino and Erik van Nimwegen
Genome Research, 2019

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:

• False discovery rate (FDR) - a number between 0 and 1 that controls the number of reported peaks. The greater the FDR the more peaks will be reported. Default value is 0.1 which means that 10% of the reported peaks are assumed to be false positives.
• Foreground and background window sizes, and window step size - The window sizes used to scan the genome to find significant ChIP-seq signal enrichment.
• Adapter sequence - Sequencing machines use a small adapter sequence that is ligated to the DNA fragments of interest. CRUNCH by default checks each sequencing read for remainders of this adapter and uses for this a small library of commonly used adapter sequences. If you are aware of the adapter sequence used in your data, you may specify it here.

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

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* 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.