Mapping with BWA-MEM

[raul]

Dear Aiden-Lab,

 

I have some questions regarding the mapping of HiC paired end reads.

My first question would be, whether are you were using BWA or BWA-MEM for mapping your data. Secondly, we did not find any option for unique mapping per se using BWA-MEM. Do you have any experience here or do you know, whether this is possible at all using BWA-MEM? What parameters are you using to make sure you only obtain uniquely aligned reads?

 

I appreciate a lot your help and thank you very much in advance for your advice.

Best,

Raul

[Neva Durand]

Dear Raul,

We use BWA mem for mapping the data, with default parameters.  BWA will align the sequence data to the genome and assign a mapping quality score, which indicates whether or not the read mapped uniquely.  We consider all reads for most stages of the Juicer pipeline, but discard reads with mapping quality 0 when we make the Hi-C map (as MAPQ 0 reads are reads that align to multiple places in the genome).  We also make a second map that contains only reads with MAPQ >= 30; this second map is what we use for feature annotation.

Please see the Juicer pipeline for more information; in particular, you can see the calls to BWA mem.  Note that it's important to align the read ends separately and combine them after the fact in order to capture the chimeric ligation events.

http://aidenlab.org/juicer/

https://github.com/theaidenlab/juicer/blob/master/AWS/scripts/juicer.sh

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org