Not getting reproducible results.

[sklasfeld]

Good afternoon,
I downloaded the 358 input bam files for Drosophila (dm3). Next I downloaded the respective umap files. Then I ran the blacklisting tool. It did not give me the same results as found in dm3-blacklist.v2.bed.gz. Is there something I am missing?

When I run the demo, I get the expected results.

I hope to hear from you soon.
Thanks,
Sammy

[sklasfeld]

Update: I realized that I need to sort all the 358 inputs and sort them. My result is closer to the one posted but it still does not match perfectly.

[aboyle]

The smaller genomes use a different overlap parameter. I recommend using 5kb instead of 20kb like was done for human. You can change this in the code here: https://github.com/Boyle-Lab/Blacklist/blob/master/blacklist.cpp#L469

[sklasfeld]

if(miss < (binSize/binOverlap + 200)) { // bridge over adjacent bins plus 100 * 200 = 20kb
I am a bit confused about this part of the code. Since we have 1000 bp bins and 100bp overlap, wouldn't the +200 part actually cover 20900bp? The comments say it only covers 20kb. Was the comment rounding?

[sklasfeld]

I changed: "if(miss < (binSize/binOverlap + 200)) { // bridge over adjacent bins plus 100 * 200 = 20kb" to
"if(miss < (binSize/binOverlap + 50)) { // bridge over adjacent bins plus 100 * 200 = 20kb"

I get closer to dm3-blacklist.v2.bed.gz, but it still is slightly different. Here is what the code now reports:
dm3_Boyle_Blacklist_359_inputs_V2.txt

The current code masks 3,284,300 bp compared to 2,689,400 bp that it is supposed to output.

[sklasfeld]

I did notice that one of the mapped input files, ENCFF620WUR.bam, used to generate the blacklist is empty when I try to download it. Could this be causing the descrepancy?

[aboyle]

Have you been able to work out the discrepancy? Perhaps we can compare md5 hashs of the bam files to make sure that we are working with the same data?

[sklasfeld]

Below are the inputs I used. I sort and index them using samtools and then run the blacklist tool.

1bda0787cf4d5cd51b9097242c871a57 ENCFF233VTH.bam ac0f8526cfb22439ae889b57b30d7768 ENCFF681BGF.bam c9bc2d5f89db104070238afe85ee2ed7 ENCFF732VPR.bam 8852656fdd8f95d79d306da6ebfb4e4a ENCFF077CZT.bam fbfc80c9d0faf591912bd4755dbb813d ENCFF147WIX.bam 134f826105b6ff8ff731d6865e75aa8f ENCFF559FVI.bam 6f97df5ed967405fea6287b0571a29e1 ENCFF601YEV.bam 52daa095fb456fd96695a16cdd8c58cc ENCFF859CSL.bam 91a78750c4578fb0c369c9cc655ff92f ENCFF742WYI.bam 61a99f49cf9abf2cd9b276250511de6e ENCFF106RDB.bam 6345e03f33c55fa181d777aa5362b224 ENCFF590ZBF.bam 4bae22d3237ee69f24ea89f39e3a0933 ENCFF131ADH.bam 960d2e614e1de9d37f844363d1240298 ENCFF629EPV.bam 70b01f58197e093b783d0d04676a3601 ENCFF700BPT.bam 70717ba428ef29ade2f57547b472cbe2 ENCFF885NVR.bam 303b40e767d32e96349ef9d04c416f3d ENCFF829TBG.bam 1f6fa7943c5e21766fc046feda7bcddd ENCFF065TJT.bam bf6538ca69f56e50c41a16a5f217d9b5 ENCFF284HMI.bam 1d648b651582d26f2dd8fa483fa2cd45 ENCFF283GTE.bam c67850b30bbf5d8ab532203abffc64e1 ENCFF306ZFT.bam 8358989370f0c58eb15c9c831d763ca3 ENCFF581RIS.bam 6916969b044faf06b1209ef474e73574 ENCFF250KKN.bam de08215c94e31c274a8529ea0260fd27 ENCFF193FPZ.bam 0435afeec25862f71a5d695ac3d0cf1a ENCFF287ASZ.bam b34092e86d80beef12f5fe70016b3dc4 ENCFF003ABI.bam 6c6fea8b632834b83f125ee91985ea4a ENCFF458DOV.bam 9f5f8445807ddf1d9b1698e318d40d4e ENCFF946AKF.bam b7783ec69431204ac2609c0705f8f503 ENCFF629EWI.bam b0c201231efe347447dc2dc6bef3b358 ENCFF394RFK.bam fd1fcfe349cba27a6b1602732d58353f ENCFF207PAC.bam 67a7e388738779873d82e6eef2bf8717 ENCFF004BRF.bam 34238b333cee345c35feaf249e35653d ENCFF824YSW.bam 6fa1c2b47cce6c3b42b4d29041c59417 ENCFF519MSI.bam d25cf0204c6ebd81cccc4bdbc78ce1d7 ENCFF593EHH.bam 8e7cac72f6f57be4dc26c280f536f840 ENCFF180OPH.bam e5c07e8bfc95f2d70d80435d7b576421 ENCFF211VGY.bam 170bc40a2a8b3b3d7c9ae6d5a06c047b ENCFF451HVT.bam 038b25636ed080a9d765b28bb9b4d008 ENCFF611QSF.bam 24d3893da8ed5562ce280cbbb00cb990 ENCFF275XWP.bam f930d6ea93917f0f88e06f9567b24bae ENCFF436TJC.bam 85a106602b62dec250d488300a5531d4 ENCFF095UPR.bam 601f9d0897dbb2a534a19e019ee8563c ENCFF761YRC.bam 088110dfd995fcbe3ce0ad5d9be7836b ENCFF628ZJC.bam 7c32ff05e55249d6a915660911983507 ENCFF870NJB.bam 01410bd84d71354e509d43da52a43f3e ENCFF131AJL.bam 0d1ceccdda7c8436fc83dd839cd99940 ENCFF388YDC.bam cb61f8823a1fe71c403ee84ec879e3ce ENCFF378VIK.bam 994184f2cfb5cf0ea1cf3822f23a31e2 ENCFF623UPG.bam bdb1c5729fe8335f90e4a235c39a299e ENCFF905JTV.bam 05302c5245e174dc44f090df50692a55 ENCFF357GXO.bam 5773d201bbf8f8433ec81e438ce31c6b ENCFF439RLW.bam 484ee5f4fe9182f1e12a9ff8831d9602 ENCFF021HGV.bam 930b7076db674ef6fc76045422b2cc77 ENCFF404BXO.bam dc8bd91feefa86cc562982400037e2ba ENCFF457DOT.bam 0d4a7e723d3442606e10716562b9e527 ENCFF785ESV.bam 66b46dcf734ecfc23f3b4c23f815d93c ENCFF499IDB.bam b137a979117e040fbf3c68075a9551a2 ENCFF786LWS.bam b601b6b3312f96324bbb42e857ad2338 ENCFF462LNZ.bam d51b28abe731d20d5f6f83df4aac26c2 ENCFF206YSR.bam 68595a7e79a5fcf2f326c9fc473b51c7 ENCFF350AFG.bam 84b1ea6107e392216661dd6e879bba4b ENCFF985ZOO.bam a82e8419c0ec3b02d6a9b6d76f5c897f ENCFF524VYT.bam ed528536a8851bfea6a39f873bc7433e ENCFF946YDY.bam 670c22c17ab3626407145f499fce1729 ENCFF713ZRN.bam e008b3d7aaeb2afc224cd911b3049b93 ENCFF714HKJ.bam 159e4b761bef5cc4fdda550ecf34d11c ENCFF659AIN.bam 5aa9cf1982984b527e8d07e1953adc19 ENCFF477KPR.bam 584e37ad703272837f736824f32b5bfc ENCFF225RYJ.bam 6e0f5b99fcf3de95d532de645796611d ENCFF189KEK.bam 3bd11b6a6fec00b7d8ee9d9c8176dc2c ENCFF114FSY.bam 1e1d041c8a26e30c2d13a5e3fbd00be3 ENCFF458QKP.bam 718cdef7472558951155157fe95e8ba3 ENCFF695DLD.bam 2b0e5aacbceaf15eaf2d49ba81198b00 ENCFF844OGB.bam 1b9edb1ad1f96492672bc2206d5b00c8 ENCFF622LBS.bam 022786fe5e6c991eb5ef2b79ea786fae ENCFF268BGJ.bam 9aea90d8808eb0421a4f93b810adce36 ENCFF005AMV.bam 5848b723b08ae343324e98084813d525 ENCFF716YQA.bam 0ce91c75db7525bebd32eecf8195fb67 ENCFF394PGP.bam 0d27e75341b47c73af32d521b8e34cb6 ENCFF967QWP.bam fc67f2006b30ade66b76570ad96a2b79 ENCFF797XKZ.bam f5f84e5237496ec28be2175b756cd279 ENCFF678CWT.bam 0193df5cb8e7ee897e5aef9f7141e49c ENCFF376HRI.bam 24f2eb0ece01bd2dfcb180b84b5af862 ENCFF557QRY.bam df8731b16de6d970df4985d6759c01d1 ENCFF819JEP.bam 9f7aea29d312d3e3846fd6fc27a52ebd ENCFF242WXD.bam 08e1c529a79752fe0d06fc8e9f79a928 ENCFF410XLO.bam 054a98db43a293d4820c6c739203e536 ENCFF538THV.bam 10a5c3cf1f372fdd0dea84ddaeab2361 ENCFF945ATF.bam 093f1d8e66c91ea7cd87e5be0ea37aa2 ENCFF383UQQ.bam 1bfb3bae63aa21d64b240f98b70edc9d ENCFF080XVM.bam 0a00cb1d4048c92b73a8592aa91f625e ENCFF065XAN.bam bccdda4bde26a7921a8b452df1e19e51 ENCFF811NMV.bam a1b3b2c811bf1ea36f00fa5ab19dcb0c ENCFF319JIX.bam 653643c85b640fd93f8d5aa63c2305c3 ENCFF958EHX.bam 6512a6414644784689c6a7af96b06a11 ENCFF222PMK.bam b045191782fe763f48d0bced01918180 ENCFF229YUF.bam 9470d523b4f5801491d72e6dbe84c814 ENCFF102IUS.bam b291018d39029225977993dd6e6eb95f ENCFF769KHF.bam 91281b0df475d5464167180f34b643d8 ENCFF502RAH.bam 503aeda34a6ee174e857e2380ba0e754 ENCFF431VPM.bam 01ef00ba6e253ed12601e00099f59918 ENCFF671SNX.bam 65596905cbb038df636296bc82ae8dc9 ENCFF328WTX.bam e27e4ba4640715842b0c38fcfbc5d0ea ENCFF649NAR.bam 55f6d86920c604c4986a18691948661b ENCFF995EVH.bam 97253a8c7421fb8438afb2f9149b1efc ENCFF454XMX.bam 088b064124d081e27a8fe3b50a0be930 ENCFF241ANI.bam 39706c551dd79bc9c33db680543f3b7d ENCFF915WNF.bam 78a16b1082b678e13aa4e3b2e85b7d10 ENCFF084WHE.bam 64bcf086f7db76335f52d705e3854550 ENCFF483ILB.bam 4d1da4afbd7db2dd8b30534bbdc3305a ENCFF387NXT.bam 04f3f7378ea6663a3511deed67a8048c ENCFF879UIL.bam 71ae43946532c66fd914aba92ef3f994 ENCFF224DXG.bam 5bee983d5ec98b4c5b3bec8ccec9a14e ENCFF223QDQ.bam bf8615912ca3af0966e281ce9bcb513c ENCFF204SVE.bam 50da260f4ee6450098741c3871fe88ec ENCFF831NLI.bam 9838027aa181f2915d8733f477b7fa40 ENCFF555XLM.bam 977dba328c935ed8697df1f2fb790b4f ENCFF896CZT.bam 5cffb7e09f2331830bb6f92ad009d687 ENCFF106WPJ.bam 2ab601ee1409385087097b3800df9e5a ENCFF679HNE.bam a746bee2bc5d6e472fc8b42f0f0b2eb8 ENCFF952QWG.bam 186221e2fa7cd590c497dce38c8c5a24 ENCFF826PNM.bam fcd3519fcff621e77ef55662920b54cd ENCFF490AYC.bam d5ea237d24447db820ed89c8735c7af9 ENCFF623CWQ.bam 4156e561e3c09a534b8f68e7324b23c3 ENCFF288TBW.bam ca1d765e308b3c6f96abf11bd1ba9818 ENCFF079JWJ.bam ed5b4a0966c2700b9badb15bd2eac50c ENCFF958HPY.bam afc9d1c61d88c65e9ccf7fd9cc78705d ENCFF733GRJ.bam 1549aa74b845583ba279581b33bce9ad ENCFF372NKB.bam 5ec6b0bd800d8e7c085e907b011ecd0f ENCFF436XZF.bam 5f02bea4600af479e083fbac423b4522 ENCFF731GVL.bam cb84f57601f831c8bbfe6972fae4257a ENCFF124CEH.bam 120ff76abedc5405ba29195cfe3518f3 ENCFF931YEK.bam 4449268f749ab631ed7e175971526f03 ENCFF418MNM.bam cbaa97d8f9d49e165e0c8d0b77df74a8 ENCFF252XEX.bam df14f95d9ef5c198f71de652b6f8e950 ENCFF696NJN.bam c041cb2eb050faac0e8fd20b6b6c5801 ENCFF373RDQ.bam beabb9db574f2c6513b3e67117ca2e03 ENCFF438IGP.bam 9ccf052127bbd7f4c1c1ed7a990e69eb ENCFF167BST.bam f6dd3a222762adf94a2428aa9132f8c0 ENCFF688RCZ.bam 465b6a650dd6829ae51ba99b26c10e5a ENCFF631LTG.bam 51ea4978e034948096b5619545d04e00 ENCFF707LKV.bam 07c4e0106a9603a8e5752e8ee99772c5 ENCFF692GXY.bam 8e252573d438f6329bc0d00c63758d9c ENCFF250GSO.bam 3436581c7423921f0d39d2651a988428 ENCFF724HJP.bam cdaf965a0d7cb99718f957db5eb67c80 ENCFF161PKG.bam ec15e7c8351544fdfed02a6cc699287a ENCFF187IPL.bam 032b130eeaf5440d81fc05b244fdd0a2 ENCFF799AXA.bam fb64e9fe63d628dc33ba3eb4a07834b9 ENCFF367FWL.bam 1e6a6ae032b2ecd5332581ba63985317 ENCFF495DBI.bam ca0631f310853d89c2709beccada7af3 ENCFF318IXH.bam a1aa5a85bb306cf0b3c6dfa9fa090164 ENCFF887XIW.bam 004ee827c9441514414a56d1743d5867 ENCFF204PNY.bam e23f3aecc8abd55df5244644f1cacb2f ENCFF923PND.bam fc2b1b49c813e6f4fea1599ef12bb51a ENCFF762FRV.bam a7be20b1834f781fb8d08b51cc019f6b ENCFF326SGK.bam 9b1a936a1a2fecdd6509508a04ebb6d9 ENCFF852KMF.bam 10f906f407d24a84b7ce950192a73da8 ENCFF645WOW.bam 7091cce03d3226af322168c35aeb059b ENCFF540KDY.bam ea9dde895ecd2562736e7f58479be244 ENCFF693TQN.bam 4859292ab313d546a1d1b20b995efba4 ENCFF187JIR.bam 0639748d13d0ed626f0ebf057e6f05a5 ENCFF865PFP.bam 5b06bae6a6fe300c3f624e45204a3882 ENCFF481KZC.bam 27f576355da05520920f45bb680f2776 ENCFF896SNN.bam e1a06378bfa3bc25a9b13b5c21953b6b ENCFF870EDO.bam af41652162045cb27b3ebdcab4619c35 ENCFF925VBA.bam 87cd8d367ed83bd21b5f1da047f6c475 ENCFF029GFM.bam d993a35ad3ac85bc7c4a3f0c1ad85e44 ENCFF855WHN.bam a3f7d17e8b835dcdbb03759689d5007b ENCFF303PXP.bam 41e4cc7f554f613a18d245fe190cf428 ENCFF140RKS.bam 92b6751b2435f8ccf0d96c28cc21bd64 ENCFF778ODE.bam 71d11836776d4997602f41664f8b218f ENCFF009ICI.bam 04000772ba7c4e3ff0831a8d29ad7692 ENCFF920YJY.bam 9db72f1bd4de99333558165b71b9d574 ENCFF620WUR.bam 08d97dac08a056fd95c26148ff3fc54d ENCFF252MYD.bam 3ac312e43f7d63a03428a56224391026 ENCFF755BUZ.bam 349963e6e042f52d05ba253c78020721 ENCFF003RFA.bam 190203061d800466affdae227e14f9e5 ENCFF729RIB.bam 9289bc064111f2fc9fd155d50dbbc0a1 ENCFF488LSG.bam 7a5d1b97b53114b3e722e19e5dc305ff ENCFF093ZNB.bam 97bc68a4bf6d4e93a03664f31e84b2a0 ENCFF613JIK.bam e7b873ed55da0b95b594ab8590f38e70 ENCFF317YMT.bam 2b7f2fc1fa80481a5ca9ad591665a198 ENCFF197CII.bam 9077eecf1ea625eb970e04b162f5c979 ENCFF631BEL.bam 45920d459469a85e396ef1743342b874 ENCFF796DUS.bam 778802038fdf09f0e7a23679c416872a ENCFF790LWG.bam d51a54230ddaa65ed60c038fcdc8d524 ENCFF582LEN.bam 4fd773cc0fa5e9c7281a40d345e306de ENCFF884GUV.bam 1a0c51f09e5d105b601d24a5496f1edc ENCFF411IHO.bam 1391ba36b7d4123b960beb1bd8861d49 ENCFF874ULN.bam 68f7054c20a33b2e7d835c247d4cd53a ENCFF857TNV.bam fff8b06efe8da1f667341263c83f85f9 ENCFF827OQY.bam a4a527d4a0c526abdef3529247fe96df ENCFF126EXP.bam d70c5ab84d1d851d633282c0fd76cfa0 ENCFF740SKA.bam e554a50b04a0cfc84b4dfc2053002390 ENCFF226UNJ.bam ce46279d0b0fbb9eba056b68fd292704 ENCFF853UTB.bam 03afd09cfbb0e8769a8eb6c3ba6e0dc3 ENCFF048THA.bam 65554822397fe1d8b45e84885cf33dc0 ENCFF119GJD.bam 43e6a828a415e40b66935f3fae06187c ENCFF397XGL.bam d7de3eb7a462824d07d48ee850159fea ENCFF779SYJ.bam 6af743f487f73bae4ad249e9074de3ff ENCFF977ELF.bam 4a0dacfad78fc28b8e162db7de5ef065 ENCFF662MLO.bam ccaa4d52e983860ab72ae026849fcc47 ENCFF645BGQ.bam aea3502e9ae506eedd6497c65f3bd3fa ENCFF018KZH.bam 55079d6a425f0dac9bcece8fb4b2e563 ENCFF491SKT.bam 47dbff4aa610b36c3afcd270feaa2db6 ENCFF815HPL.bam 0120cb96fe74d806314eb100f3eed8f9 ENCFF152ZSD.bam caa76bcfc7db963c660fe9ceaf5d0424 ENCFF395KVD.bam eef88c96e95cfae4b074dccb3f7f0deb ENCFF809YSN.bam 5472425e17295d80ccf8cfb798b380bb ENCFF256ZSM.bam 66b62fbd08abf4fc8a1a629503445e09 ENCFF874BBH.bam 849d16431663e32c9454d6aa370b473b ENCFF221KJF.bam 28d85080faf3ea09c3ec11a76bd5d00f ENCFF327UKB.bam 321e99bc1d2355983dc15941a4e23a71 ENCFF998LJN.bam f45b1aa3a29378666a653c3ceda2ed76 ENCFF301QVG.bam 8b0258ba95feae7c5f864959d0b293d7 ENCFF687BSO.bam 89bd4e0c66b9bffe54e3837bf699fdf3 ENCFF353FUD.bam 5760e5be3a194986d60e6572ebffebcb ENCFF860QFY.bam c3f4ff4d0c7aad31ea6495d1cbe56ff4 ENCFF345FVS.bam aecd51a424880ef83df8184d08245e30 ENCFF877KDY.bam 881db6d8ba1ea54d1efaef10c2ddefba ENCFF037UMY.bam 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