Brandon:LabNotes/Project1/2012-3-6
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peak calling software[edit]
- peakseq seems okay
- try out macs and compare. macs seemed to call the most peaks, in papers found peak calling algorithms comparisons
- all peaks found by macs were found by the other algorithms. peaks in other programs were not found by macs. false positives?
- Though peakseq seems less stringent, didn't call many significant peaks when control and sample are analyzed. Also probably many more false positives.
macs14 versus peakseq[edit]
- macs14 features
- single sample and sample/control analysis possible
- macs14 also gives negative peaks (ones with more reads in controls)
- macs14 outputs files in easier to retrive/analyze format
- outputs usable bed files (use with bedcoverage or to visualize on UCSC)
- macs functions better with smaller datasets/reads amounts (then peakseq)
- gives fold difference in number of reads in the comparison
- analysis with nextera samples 1 as sample and 4 as control were done, 500 cells sample
- all peaks called in peakseq were found on macs14.
- peakseq found 31 peaks, macs14 found 637 peaks.
- validated peaks in UCSC genome browser with BED file. All with FDR of 0 had more reads in the undigested sample than protease digested control. did with peaks that had least fold different, and most significant peaks.
- used bedcoverage
' | peakseq | macs |
peaks_called | 31 | 901 |
bases_covered | 18007 | 539451 |
macs_onto_peakseq_500_cells | 100% | |
peakseq_onto_macs_500_cells | 3.33% | |
analysis only with macs14[edit]
- did macs14 analysis on raw UCSC GM12878 data and nextera tagmentation samples 1 and 4.
macs14 peak calls (macs only anslysis) | ' | ' | ' | ' | ' |
covered_bp | total_bp | % covered | |||
ucsc_onto_500cells | 182515 | 539451 | 33.83347144 | ||
500cells_onto_ucsc | 182515 | 82252260 | 0.221896638 | ||
. | |||||
peakseq peak calls (peakseq only analysis) | |||||
. | covered_bp | total_bp | % covered | ||
Peakseq done on raw UCSC data | UCSCv1 | UCSC v 500 cells | 2115 | 18007 | 11.74543233 |
Peakseq done on raw UCSC data | UCSCv2 | UCSC v 200 cells | 1022 | 6718 | 15.21286097 |
Peakseq done on raw UCSC data | UCSCv3 | UCSC v 100 cells | 1263 | 7047 | 17.92252022 |
- macs seems to call peaks of the same peaks, have 33% of the same bases covered when ucsc peak calls are mapped onto 500 cell peak calls.(probably consistently open peaks in lymphoblasts)
- even if dataset is reduced for mapping 500 cell peak calls into UCSC peak calls, % covered would still be .2% to .3%. shows that datasets are very different.
- this differs from peakseq calls, which had 11% same peak areas called. probably more non specific peak calling. non specific peak calling has been shown in other papers.
- compare to previous peakseq data analysis
conclusions[edit]
- as seen before seems that with nextera data, the cell lines are different and thus wont have much reproducibility in terms of accessibility.
- macs calls more peaks that are accurate, since 33% of those called in 500 cell accessibility data are present in UCSC data.
- all calls in macs were in peakseq. but only a small number of calls in peakseq were in macs.
future[edit]
- will read macs14 paper to get better understanding.
- peakseq can be used as vaidation for top peaks.
- Useq is comparable to macs14, could also test that out but macs seems best right now. still should look at other programs
- can do replicates analysis as done here: previous peakseq data analysis