macs2 callpeak其中的一個參數(shù)-g古掏，設(shè)置有效基因組大小，
-g GSIZE, --gsize GSIZE
Effective genome size. It can be 1.0e+9 or 1000000000,
or shortcuts:'hs' for human (2.7e9), 'mm' for mouse
(1.87e9), 'ce' for C. elegans (9e7) and 'dm' for
fruitfly (1.2e8), Default:hs
根據(jù)教程Introduction to ChIP-Seq using high-performance computing跳轉(zhuǎn) https://deeptools.readthedocs.io/en/develop/content/feature/effectiveGenomeSize.html匀钧，
Option 1 faCount翎碑，下載后文件改為可執(zhí)行，即可使用之斯；原理是除了N之外的堿基數(shù)統(tǒng)計日杈，適用于multimapping reads存在；
Option 2 unique-kmers.py佑刷，pip install可安裝莉擒，但發(fā)現(xiàn)集群里有，直接cp到我的目錄下使用瘫絮；MAPQ等方法過濾后適用涨冀。
也可在khmer github下載 https://github.com/dib-lab/khmer/tree/master/scripts
【測試1】玉米參考基因組
[Option 1] Chr1-10 ATCG和為2,075,605,238，約為2.1e+9
$ ./faCount ./genome/b73_v4/Zea_mays.B73_RefGen_v4.dna.toplevel.fa
#seq len A C G T N cpg
1 307041717 80478275 71219187 71150610 80507052 3686593 13339729
2 244442276 63816849 56413504 56401383 63899356 3911184 10584323
3 235667834 61901922 54630954 54743629 62016611 2374718 10187767
4 246994605 64920679 56483306 56568849 64972046 4049725 10363139
5 223902240 58581754 51738109 51824187 58686601 3071589 9668744
6 174033170 44854954 39770359 39762960 44889331 4755566 7477887
7 182381542 47921757 42102677 42136861 47989908 2230339 7821653
8 181122637 47395194 41973473 42016725 47335775 2401470 7901594
9 159769782 41740561 36929012 36963464 41696724 2440021 6943031
10 150982314 39591853 34987130 34981695 39609962 1811674 6554095
Pt 140384 43281 26908 27087 43108 0 4429
Mt 569630 159353 125604 124652 160021 0 20332
......
total 2135083061 558869376 492941406 493261213 559278187 30732879 92095961
[Option 2] 約為1.8e+9
$ ./unique-kmers.py -k 150 ./genome/b73_v4/Zea_mays.B73_RefGen_v4.dna.toplevel.fa
|| This is the script unique-kmers.py in khmer.
|| You are running khmer version 2.1.1
|| You are also using screed version 1.0.4
||
|| If you use this script in a publication, please cite EACH of the following:
||
|| * MR Crusoe et al., 2015. http://dx.doi.org/10.12688/f1000research.6924.1
|| * A. D?ring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11
|| * Irber and Brown. http://dx.doi.org/10.1101/056846
||
|| Please see http://khmer.readthedocs.io/en/latest/citations.html for details.
Estimated number of unique 150-mers in ./genome/b73_v4/Zea_mays.B73_RefGen_v4.dna.toplevel.fa: 1767458681
Total estimated number of unique 150-mers: 1767458681
【測試2】GRCh38麦萤，給的參考是Option 1為2,913,022,398鹿鳖，Option 2為GRCh38（Read length 150）為2,862,010,578
和我計算的差別不太大。
[Option 1] Chr和為2,934,860,425
$ ./faCount ./genome/Homo_sapiens.GRCh38.dna.toplevel.fa
#seq len A C G T N cpg
1 248956422 67070277 48055043 48111528 67244164 18475410 2375159
2 242193529 71791213 48318180 48450903 71987932 1645301 2192670
3 198295559 59689091 39233483 39344259 59833302 195424 1673293
4 190214555 58561236 36236976 36331025 58623430 461888 1503429
5 181538259 54699094 35731600 35879674 54955010 272881 1566535
6 170805979 51345477 33646690 33713330 51373025 727457 1511189
7 159345973 47058248 32317984 32378859 47215040 375842 1622825
8 145138636 43333530 29030173 29103787 43300646 370500 1338200
9 138394717 35736329 25099811 25170662 35783748 16604167 1255728
10 133797422 38875926 27639505 27719976 39027555 534460 1388978
11 135086622 39286730 27903257 27981801 39361954 552880 1333114
12 133275309 39370109 27092804 27182678 39492225 137493 1315968
13 114364328 30047611 18839192 18933605 30162717 16381203 842469
14 107043718 26673415 18423758 18559033 26911943 16475569 895881
15 101991189 24508669 17752941 17825903 24553812 17349864 906026
16 90338345 22558319 18172742 18299976 22774906 8532402 1150891
17 83257441 22639499 18723944 18851500 22705261 337237 1248328
18 80373285 24050680 15794455 16061651 24182819 283680 756014
19 58617616 15142293 13954580 14061132 15282753 176858 1105620
20 64444167 17867246 13916133 14094472 18066406 499910 773477
21 46709983 11820664 8185244 8226381 11856330 6621364 462299
22 50818468 10382214 9160652 9246186 10370725 11658691 634646
X 156040895 46754807 30523780 30697741 46916701 1147866 1322709
Y 57227415 7155845 4632232 4630489 7217789 33591060 169449
......
total 63147197748 913598440 635211771 638005906 916191480 60044190151 31647338
[Option 2]
$ ./unique-kmers.py -k 150 ./genome/Homo_sapiens.GRCh38.dna.toplevel.fa
|| This is the script unique-kmers.py in khmer.
|| You are running khmer version 2.1.1
|| You are also using screed version 1.0.4
||
|| If you use this script in a publication, please cite EACH of the following:
||
|| * MR Crusoe et al., 2015. http://dx.doi.org/10.12688/f1000research.6924.1
|| * A. D?ring et al. http://dx.doi.org:80/10.1186/1471-2105-9-11
|| * Irber and Brown. http://dx.doi.org/10.1101/056846
||
|| Please see http://khmer.readthedocs.io/en/latest/citations.html for details.
Estimated number of unique 150-mers in ./genome/Homo_sapiens.GRCh38.dna.toplevel.fa: 2882789054
Total estimated number of unique 150-mers: 2882789054
