Open trotos opened 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.
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?
Thanks for the suggestion - I will look into these alternative methods for mapping.
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.