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rr1859 / R.4Cker

MIT License
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reduced genome, Bowtie command clarification. #28

Open trotos opened 7 years ago

trotos commented 7 years ago

Hi, could you please explain why we need a reduced reference genome? Is it not possible to map the 4C to the whole reference genome and then proceed? Also, at your bowtie2 command you trim the first 26 bases, I expect that those are the adapter and RE that needs to be removed. So depending on the experiment those could vary.

rr1859 commented 7 years ago

Since we expect the ligated interactions to always be adjacent to a RE site we map the reads to a reduced genome and gets rid of any spurious ligation events. The bowtie2 command is specific for the example and yes it should be changed according to your samples.

trotos commented 7 years ago

thank you for your answer, so you clean up your mapped reads in a more efficient way (mapping tools) than using R. But I got a follow up. I've noticed that using >50 nt length for mapping is inefficient and sometimes when usable reads shorted inadequate. I am using instead bowie v (1.2.0) or bwa aln (>0.6). Overall mappability is greater (especially when read lenght is < 30 nt). So, maybe it would be favorable to add those options?

rr1859 commented 7 years ago

Thanks for the suggestion - I will look into these alternative methods for mapping.