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|04-15-2012, 08:05 AM||#1|
Join Date: Sep 2009
MNase-seq data analysis
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.
|04-21-2012, 06:13 AM||#2|
Location: 45°30'25.22"N / 9°15'53.00"E
Join Date: Apr 2009
|12-04-2012, 10:19 AM||#3|
Join Date: Feb 2012
python2.7 danpos.py tagAlign1-tagAlign2 -k 1
danpos version 2.0.1
python danpos.py tagAlign1-tagAlign2 -k 1
Namespace(bg=None, clonalcut=1e-10, count=None, distance=100, edge=0, extend=80, fs=None, gapfill=0, height=5, keep=1, lmd=300, mafrsz=250, mifrsz=50, name='result', nor='F', paired=0, path='chr22.Gm12878.nuc.tagAlign-chr22.K562.nuc.tagAlign', pcfer=0, smooth_width=20, span=10, statis='P', testcut=1e-05, width=40)
time elasped: 0.36073589325 seconds
normalizing wigs ...
less than 2 datasets, no normalization to be done
saving normalized wigs ...
time elasped: 0.360930919647 seconds
pooling each group ...
Traceback (most recent call last):
File "danpos.py", line 125, in <module>
File "danpos.py", line 122, in runDANPOS
File "functions.py", line 262, in danpos
IndexError: list index out of range
Am I missing something in terms of being able to tell DANPOS that these are the two files I want to compare nucleosomal positioning data on?
Please help, urgent