The bowtie_results folder contains the results of the reads mapping. The results of first mapping step are available in the bwt2_glob folder, and the seconnd step in the bwt2_loc folder. Final BAM files, reads pairing, and mapping statistics are available on the bwt2 folder.
The read mapping statistics are represented as a barplot of the fraction of aligned R1 and R2 reads. The first bar represents the overall mapped reads fraction, and the second bar distinguish both mapping steps.
Mapping statistics are available in the ‘.mapstat’ files. The total mapping statistics per sample are available in the ‘SAMPLE_NAME.mmapstat’ file.
Usually, a high fraction of reads is expected to be aligned on the genome (80-90%). Among them, we usually observed a few percent (around 10%) of step 2 aligned reads. Those reads are chimeric fragments for which we detect a ligation junction. An abnormal level of chimeric reads can reflect a ligation issue during the library preparation.
Once R1 and R2 reads are aligned on the genome, HiC-Pro reconstruct the pairs information. The pairing statistics are summarized in the plot below and available in the ‘.pairstat’ files. The combined pairing statistics per sample are available in the ‘SAMPLE_NAME.mpairstat’ file.
The fraction of singleton or multi-hits depends on the genome complexity and the fraction of unmapped reads. The fraction of singleton is usually close to the sum of unmapped R1 and R2 reads, as it is unlikely that both mates from the same pair were unmapped.