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Valid pairs detection with HiC-ProĮach aligned reads can be assigned to one restriction fragment according to the The sum of unmapped R1 and R2 reads, as it is unlikely that both mates from the The fraction of singleton is usually close to The fraction of singleton or multi-hits depends on the genome complexity and An abnormal level of chimeric reads can reflect a ligation Those reads are chimeric fragments for which we detect a Among them, we usually observed a few percent (around 10%) of step 2Īligned reads. Usually, a high fraction of reads is expected to be aligned on the genome *.mapstat - mapping statistics per read mate.
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*bwt2merged.bam - merged BAM file after the two-steps alignment.*_trimmed.bam - Alignment of trimmed reads.*_trimmed.fastq - Trimmed reads after end-to-end alignment.*_unmap.fastq - Unmapped reads after end-to-end alignment.*.bam - Aligned reads (R1 and R2) from end-to-end alignment.If -saveAlignedIntermediates is specified, additional mapping file results *bwt2pairs.bam - final BAM file with aligned paired data.Note that if the -dnase mode is activated, HiC-Pro will skip the second Singletons are discarded, and multi-hits are filtered according to the Second, reads spanning the ligation junction are trimmmed from their 3' end,Īligned reads for both fragment mates are then paired in a single paired-end The current workflow implements a two steps mapping strategy. Using Hi-C data, each reads mate has to be independantly aligned on the The current version is mainly based on the Export - additionnal export for compatibility with downstream.MultiQC - aggregate report and quality controls, describing.Pipeline overviewĪnd processes data using the following steps: All paths are relative to the top-level results directory. The directories listed below will be created in the results directory after the pipeline has finished. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. This document describes the output produced by the pipeline.