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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Allowing multimapping reads #234

Closed abhisheksinghnl closed 5 years ago

abhisheksinghnl commented 5 years ago

Hi,

I have a polyploidy genome from plant on which Hi-C experiment was performed.

My question is, does Hi-C pro allows multimapping reads?

The other tools like hicexplorer discard my multimapping reads and that is not ideal for my analysis.

Thank you

nservant commented 5 years ago

Hi, Yes it does since the last version. HiC-Pro is using the bowtie2 mapper which randomly report one position in case on multiple mapping sites. If you set RM_MULTI = 1, these reads are discarded. But if you set RM_MULTI = 0, they are kept and therefore used to build the contact maps.

Note that this solution is not perfect, as bowtie2 chooses a random position (among all the good ones) on the genome. For instance, a more sophisticated approach could be to choose the read1/read2 position which are the closest ... and therefore more likely to be ligated together. But even if this is not perfect, it should allow you to move a bit on the repeats issue. All the best N