Hi,
Has anyone ever played with the MNase-seq datasets?
I got some mouse datasets running but there seems several points should take into consideration:
1. repetitive region: as about 50% of genome is repetitive sequence and these can arise those multiple alignments during the mapping stage. Generally, only uniquely mapped reads were filtered out for the downstream analysis, which means we lost about 50% region's information of the genome. That's critical if we want to see how about the repeat regions happened in the cell. I don't know if anyone did similar analysis and added the multi-reads and how to process them.
2. input signal: in general ChIP-seq data, the control might generates some peak signal and one of the reason arise this is due to the open chromatin structure. But in this case, say, if I notice the input sharp signal, still, that might be due to the open chromatin in that region, yet might also be generated due to other unknown reason. Has anyone also crush similar problem and how to process them?
3. peak callor choice: there are several peak callers for the mononucleosome calling, I'm just wondering whether MACS can also accomplish this if I'm not only interested in the mononucleosome peaks.
Welcome any kinds of communications and suggestions.
Thanks!
lix
Has anyone ever played with the MNase-seq datasets?
I got some mouse datasets running but there seems several points should take into consideration:
1. repetitive region: as about 50% of genome is repetitive sequence and these can arise those multiple alignments during the mapping stage. Generally, only uniquely mapped reads were filtered out for the downstream analysis, which means we lost about 50% region's information of the genome. That's critical if we want to see how about the repeat regions happened in the cell. I don't know if anyone did similar analysis and added the multi-reads and how to process them.
2. input signal: in general ChIP-seq data, the control might generates some peak signal and one of the reason arise this is due to the open chromatin structure. But in this case, say, if I notice the input sharp signal, still, that might be due to the open chromatin in that region, yet might also be generated due to other unknown reason. Has anyone also crush similar problem and how to process them?
3. peak callor choice: there are several peak callers for the mononucleosome calling, I'm just wondering whether MACS can also accomplish this if I'm not only interested in the mononucleosome peaks.
Welcome any kinds of communications and suggestions.
Thanks!
lix
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