modkit
modkit copied to clipboard
nanoporetech
Support for generic MM tags?
Hello,
I have a BAM file with MM tags of the form "MM:Z:N-21891" for m6A. modkit throws the following error:
failed to get modbase info for record 2f9765ad-b38c-49f8-80e0-4f5a0656c981, Bad Input: malformed MM delta list
Is there an option to make modkit parse such a BAM file? A few sample reads are show below. Thanks a lot!
f4b69c94-578c-4fd2-b487-0edd5cc81f05 16 1 4490935 60 1S34M1D83M1D9M1D7M1D8M2D4M1I9M1D8M3D17M1D13M2D12M1D18M2D36M1D48M2D31M5D83M1D12M3D11M1D4M1D3M2D15M1D56M1D21M1D31M1D24M1D10M2D26M2D22M1D4M1D34M2D24M1D97M2D21M1D8M1D18M1D5M1D4M1D24M1I10M1D7M1D53M3D14M1I49M1D15M1D63M2I5M1D6M1D14M1D29M1D9M2D6M1I13M1D30M2D17M2I15M1D17M1I12M1D41M2D2M1D8M3I4M2D9M1D15M4D4M1D4M1D27M1D15M5I31M1I29M2D11M1D7M1D5M2I5M1D50M3D18M4D27M1I6M2D13M4D4M1D18M431N6M3D25M1I12M1D11M1D24M1I19M1I15M1D14M1D13M3I15M1I17M117S * 0 0 AAGTCACAACACAAACTTTATTTTGATTAGTTTCTTGACTCTAAAATTGTAGGAATTAAAGGCAAATTTTGTGGGAAGTGGGATCAAGACTTTTGGAAAAAAAGACAAACTGGAAAGAATATATCTGAAAGCTCTTTGGCAGGTCGAAGATGACTGAAATCCGATTTTGAACAGCCTCATTAAGTGTACAGAATAAAACATTTACAAATCATTTTTAAAAACCAATTTGGAATGTACATAACAAGTTCATCTTTTAAGAATTTTCTCAGAACAATTATATCACATTTGAACACCCCGCTGTTTGTGTTGGGTTTCTTAGATGCATTTTCTTACCATTGTAAATGAAAATTTTACAATTAAGTATACACTTCTAATTGTATAATACTTACTGTTGATCTCAAATTTGATAAAAATCGATGCGAAGATTTTAAAAATCCAGGATTTATTAAATTGAAAACACGCATGACAAATTTCTCTAGATCAATACACTTTCAAGAAATGGAATAAGTCAGTGAGATATTTTAAACTGGCTAAAACTGGACAGGATTGTGGGGAGCAAGTCCCTCAAGGCATTTAAACAAAAATCTCGTGTAGCCCCTAACTGTTCAAGGCAGACAAAATAAATTACCATAAATTATGCCAAGGCAACTTAAAAACAAACGCTTGACGCTAAGGATTTCCTTAGCGCTTCCAGGTTGTGTAACACTGCTTCTGGCCCTAGGTCGGGACGGCAACCGTCAAATGTCGGGGTAGTTGCAATAGTAGACCGCTGAGCTAGCGTCGGACACCACGGAGGAAATGGCTCTGAGGCTGTCTGTGGTTCACTCCGCAGTCGTGCCCTGGTAGGAAGACCCATCTCGGGCTATACCAAAGGCAGATACTGTTCGAATTCCATGACGGTCCACCTCCCTAGGGCTCAGAGGGCTGGTTGGATTCCGTGCCATCCCGGCAGGGCCGTGCCTCGGGAGGCGAAGGTTGCCCGGGGGCCGTGCGCTGGGTGCTGCTGCTGCGGTGGCGGCGGCGGTGCCTGCGTTGCAGCGGCTGCTGGGATGCGCGTGGAAACCGCGCCCCGCACTTGCGGCGGGCGAGCCGATCGCGCCGTAGTACAGGTGTGCAAGCGCTGGGGGCGCCAGGATCCCGGCATCGCAGGGCCCGAGAGGTCCGGCCCACTCGCGGGGCCAAGCGGGCGGCTCTCGGACACTGCATAGTCCCAGACTGGAGCGTGTGTAGGTGCCGGCTGCCGCGGGCAGTCCCCTGGAGCGGGGCTGCAAAGAAGAGCCGGGCCCTGTCCGCGCCATCCAGCGGGAATGGGTCTGGAGTGGGCAGAGGAGCATCGAGCTTTGCGGGCGCCCAGTCCTGGCAGTCCCGATGGGGCCATAGCGGAGACATCAGCTGAGGACCGGCCGATAGCCCGGCTCCGGGAGTGGAAAGGCAGACCCAGGCCATCCATGGCCACAGCGGCCGCCCTCGGGAGCCAGCGCGCCGGTGGGGCTCGACAAAGCGTCAGGAAGAGCCTCCTCCACCCGCTTCATGCGCTTCACCTGCTTGCGCCGCCGCGGCCGGTACTAGTTGGGGAGAGCCTGCGCTGCACGCGCAGCCGCTCGGCCTCTTCCCACGAGGCCGCTTCTCTGGGTCACGCCTTCCAAGACTTGCCTAGCATGCTTAGCTCTGCGTTGTGCAGATCTTGGGTTCTGCTGGCTAACCGCTTCGTTCGTCTTTGGCCCACACCATAGAAGGCGTTCATCGGCCGCCGGGATGCAAGACTCCGTTTGGCTCGGCCCGCGTCCCAGCTGGCTTTGCCCCGCTACTCGCCAACCACCTCGCCTTTCACATCCCAGAGGCTCAGAGGCTCTCTACCTCCCCGGCCCAGCGTGCGTGAGCTGTATGGTATTGGCTGTGAGGCCAGGAAGTAGTAAGTTTGGAAAGGCGGCTGGGGCTGATGCTGCAA * NM:i:177 ms:i:1393 AS:i:1337 nn:i:0 ts:A:+ tp:A:P cm:i:221 s1:i:1140 s2:i:0 de:f:0.0677 cs:Z::34-c:63*ga:11*at:7-g*ta:8-a:7-t:8-gt:4+a:9-a:8-aat:17-a:13-ta:12-g*ta:10*ga:6-at:31*ga:4-t:48-ta:31-aagaa:59*tc*ta:22-g:12-gat:11-t:4-g:3-ga:15-a:56-a:21-t:31-a:24-c:10-gt:26-ta:22-a:4-a:34-aa*gt:23-c:8*ta:77*ct:1*ta:8-ga:1*at:19-t:8-g:18-t:5-a:4-g:21*ga:2+a:10-c:7-a:6*ta:34*ac:1*at:9-ggg:14+g:49-g:15-g:3*ta:41*cg:17+gt:5-g:6-g:14-c:21*ga:7-c:9-at:6+a:13-a:17*gc:12-aa:14*ct:2+cg:15-c:17+g:7*tc:4-c:3*ag:14*ga:3*tg:3*ct:14-gt:2-c:1*ga:6+ttt:4-ga:9-c:15-agtg:4-c:4-g*ta:14*gt:11-g:15+ggagt:31+a:16*cg:1*ac:10-cc:11-g:1*ga:5-g:5+ag:5-c:50-ttg:9*ta:1*ga*tg:5-atat:27+c:6-ag:13-ccaa:4-a:18~ct431ac:6-tct:25+t:12-t:2*ct:8-g:24+g:19+g:6*ga:8-c:14-a:6*ga:6+ttt:15+a:17 rl:i:0 MM:Z:N-21891,258,55,54,214,8,41,28,32,41,47,259,16,62,6,208,43,51,196,4,5,54,126,87,26;N-17802,130,61,21,8,65,136,48,73,2,87,138,25,175,62,38,70,52,451,11,6,87,11,48,55,5; ML:B:C,7,23,245,191,235,9,254,31,141,12,27,251,164,13,112,255,8,1,94,13,188,122,50,2,13,89,222,2,11,42,71,12,87,24,0,5,36,17,56,106,6,0,168,21,248,1,49,11,113
8ddc0184-ef2f-4cfd-8fd8-68e8d70b2b04 16 1 4491383 60 3S28M1D37M2D4M1D6M2D12M1D22M2D28M2D11M2D15M1D5M3D11M1D8M1I12M1I8M1D14M1D15M1D26M1D3M3D2M1D44M3D3M5D30M1D31M1I4M1I21M1D38M1D5M1I23M2D4M1D22M3I23M1D24M1I52M1I17M2D5M2D5M2D20M1D9M1D13M1D7M2D10M2D74M1D8M4I11M1D5M1I5M1I2M2D21M1D12M1D7M5D10M65N4M2I7M6I1M2I5M1D9M1D8M1D14M1D1M2D22M1I7M1I3M1I21M2D21M1I1M1I2M1D9M1D6M7D2M3D48M1D12M1D2M1D4M2D11M4D2M1D45M1D26M431N2M1I5M1D17M1I38M1D20M3I10M2I6M1D15M1I12M1D7M1I11M1D27M1D16M1D14M1D29M2I6M1D40M1I13M3D18M1D17M1D2M5D4M1I15M11S * 0 0CTTTTTTTAAAGGATTCCAGGATTTATTTAAATTGAGAAAACACGCATGACAAAATTTCTCTAGATCAACACTTCAAGATGGAATGAGTCTTGAGATATTTTAAAACTGGCTAACTGGACAGTGATTGTGGGGAGTAAGTCTCAAGGTATTAAACAAAAATCTCGTTAGCCCAACTGTTCAAAGGCAGACAAAAATAAATTACTGTTAAATTTATGCCAAGGCAACCAAAAACAAAACAGCAGACGCTAAGGATTTCCTTAGCGCTTCAGGTTGTAACACTGCTTCTGGCCCTCGGGTCGGGTCGGCAACCGTCAATCGGTTGCAATAGTAGACCGCTGAGCTAGCGTCGACACCACGGAGGAAATGGCTCCGTGGCTGTCCGGATGTGGTTCACTCCGCTGTCGTGCCCGGGTGGGGAAGACCCATCTCGGGCTTATACACAAAGGCAGAATACTGTTCGAATTCCGTGCGGTACCTCCCTAGGAGCTCTTAGGGCTGGGAATAGGATTCCGTGCCATCCCGGCAGGCAGAGCCTCGGGGAGGGGCGAAGGGTTGGCCCGGGCCGGGCGCTGGGAGAGGCTGCTGCTGCGACGGCGGCGGTGCCCAGCGGTTGCGGCGGCCTGGGAGCGCGGAAACCGCGCCCCGCACTTCGGCGGGCGGCTCGTCGCGCCGAGTACAGGCTGAGCGCTGGGGCGCCAGGATCCCCGGCATCGCAGGGCCCGGAGGGTCCGGCCCTACTCGCATGGGGCCAGCGGGCGGCTCTTGGACACTATCGGCATAGTCCGAACTGGAAGCGTGAAGTAGGTGCCGGCCGCCGGGCATGCCCTGGCAGCGGGCTGCAAGCAGGGCCTGCCAACAGTCCCAATTTTTGCGGCAGCCCGATAGTGGGGCCCAAAGCGGAGACATCACAGGGCTGGCCGGATAGCCCGGCTTCTGGGAGGAGAGCAGACCCAGGCCATCCATGGACGCGGCCGCCCTCGGGACCAGATGCCGCCGGCCTGGGCTCGCCAGGAAGCCTCCCTCCACCCGCTTCATGCGCTTCACCTGCTTGCGCAGAGCGGCCGGTACTGAGTTGGTGGTCCTGCGCGCACGCGCAGCCGCTCGGCCTCTTCCACGAAGGGCCGCTTCTCTGCATGGTCAACGCCTTCCAAGACTTGCCTCGGCATTTGCTTAGCTCTGCGTTAGTGCAGATCCGGGATCTGCTGAACCAGCTGCTTGCGTTATCTATGGCCCACACCATAAGGCAGGTGTTCATCACGGCCGCTGATGCTGGACTCCTCCCCAGGCTCGGCCGACGTCCCCGGCTGGCGCCCTCTACTTGCCACCACCCTGCCTTTTCGTCGGCATCCCCGAGGGGCTCAGGGACTGCCCCAGGGACAGGGGCCCAACCCTGCCAGCCCACTGGGGCTGCGCGCTCCGGGGCTGGCTGTGGTCGTCACTGGCGATATCCCGCATCTGTGCTCATGGCTCTCCAGACTACCTCGGATTCTACTTGGGGAGCACGCCGCTTCCCCCTGGCCAGGACT * NM:i:251 ms:i:872 AS:i:767 nn:i:0 ts:A:+ tp:A:P cm:i:102 s1:i:595 s2:i:0 de:f:0.1207 cs:Z::4*at:3*ag:19-g:37-at:4-t:6-aa:7*ag:4-a*gt:21-aa:23*ct:4-cc:7*ct:3-ta:15-g:5-cct:11-g*ta:7+a:12+t*cg*at:6-a:14-t*tc:14-t*ta:25-c:3-gaa:2-g:22*ag:21-atg:3-gggta:30-g:31+c:1*tg:2+t:1*at:12*at:6-t:3*tg:3*ag:30-g:5+a:23-cc:4-c:12*at*gt*ta:7+gaa:1*ta:21-g:14*ag*ga:8+g:5*cg:2*gc:6*tg:8*ta:1*ca*tg:8*gt:1*tc:1*ga:11+c:2*ta:8*ag:5-tg:5-gt*ta:4-gt:20-g:9-a:2*ct:1*ag:8-t:7-gt:2*at:7-gg:33*ag*ga:11*ct:27-a*ct:7+atcg:11-g:5+a:5+g:2-gt:21-g:1*cg:10-g:7-aaaga:4*ca:3*tc:1~ct65ag*ct:3+aa:7+aatttt:1+gc:5-t:9-g:8-t*ga*ta:12-g:1-gg:3*ag:1*ct:16+t:2*ct:4+g*ag:2+a:21-cc:21+g:1+t:2-g:9-g:6-gacgaga:2-gtg:46*ca:1-c*ca:11-t:2-t:4-gg:11-atat:2-t:45-c:2*at:23~ct431ac:2+c*ag:4-c:17+a:9*tc:3*ta:7*ta*ga:3*ag:1*ct:9-c*ga:3*ta:15+ggc:3*ct:6+ca:6-c:1*gt:5*gt*ag:6+t*gc:1*tc*tc*ta:7-c:7+c:11-c:3*gt:5*ct:9*tc*ct:6-c*at:1*cg:1*tc*tg*ag:9-g:14-c:1*gc:27+gc*tc:3*ct:1-c:24*cg:15+a:11*ct:1-ggc:18-c:1*gt:3*ct:2*ag*ga*ct:3*ga:2-a:2-gccac:4+g:15 rl:i:0 MM:Z:N-21891,328,59,57,219,10,26,39,53,254,15,66,10,201,37,50;N-17802,72,126,59,24,7,68,139,41,69,2,172,26,169,65,37,76,43; ML:B:C,119,49,2,184,238,244,245,255,22,252,156,143,249,77,81,84,35,75,160,15,9,10,17,69,142,2,14,202,10,23,151,59
450a0665-9fd7-4697-805b-a16011b7070d 16 1 4491387 60 8S19M1D9M3D32M1D10M1D18M1D7M1D20M1D6M1I12M1D10M1D10M1I23M1D4M1D8M1D28M1D7M1D21M1D4M1D10M1I8M2D27M1I1M1I41M2D7M4I4M1I14M2D4M1D20M1D9M1I11M1I9M10S * 0 0 ATTAAATAAAAAAAATTCCAGGATTTATTAAGATTGAAACACGCATGACAAAATTTCTCTAGATCAGTCACTTTCAAGAATGGATTAAATCAGTGAACAGTTTAAACTGGCTAAAACTGGACATGATTGAAGGGGAGCAAGTCCTCAAGGCATTAAGACAAAGAATCTCATGTAGCCCCTCAACTGTCAAAGACAGACAAATAAATTACCATAAATTATATGCCAAGCAACTTAAAACAAAACAGCTTGACGCTAGGATTCCTTAGCGCCTTCCAGGTTGTGTAACACTGCTTCTGGCCCTCAGTGATCGGGTCAGCAACTGTCAAGTGTCGGGGTAGTAGCAAATGTACCATTGTGAAAGCTAAGCGTCGGACACCAGAGGAATGGCTCCGTGGCTGTCTGGATGATCACTTCCGCAGTCGTGGTCCCTGGTTGGAAAACCT * NM:i:60 ms:i:253 AS:i:249 nn:i:0 ts:A:+ tp:A:P cm:i:25 s1:i:160 s2:i:0 de:f:0.1174 cs:Z::5*ga:13-t:9-aga:30*ag:1-a:10-a:6*at:3*ga:7-g:1*tc:1*tg:3-a:20-g:6+a*ta:11-c:10-t:4*ag:5+g:6*ga:16-t:4-g*ta:1*ga:5-a:28-g:7-a:21-a:4-t:10+c:8-aa*gt:26+t:1+a:7*ga:5*ct:5*ag:12*ta:4*ta*at:2-ag:3*ga*ct:2+tgaa:4+a:14-cg:4-a:20-a:2*gt:1*ta:4+t:11+g:9 rl:i:0 MM:Z:N-21891,17,18,7,256,51;N-17802,63,53,107; ML:B:C,6,218,130,199,7,94,3,17
05b73ba3-6917-4ad9-b6f7-fdd06c6893ea 16 1 4491397 60 7S45M1I39M1D3M2I14M1D11M1D6M1D12M2D14M1D16M4D7M1I4M1D5M1D1M1D24M1I59M1D47M3D3M2D13M2D49M1I4M2D44M2I20M1I19M6D22M1I5M1I29M1D11M1D23M1D5M1D78M1D6M1I42M1D14M1D20M1D15M1D2M2D53M1D20M1I2M3D17M2D2M1D53M2D27M2D6M1I2M1D9M3D25M1D63M1D35M1I34M2D12M1D22M3D17M1I78M431N28M1I77M * 0 0 CTTTTTTCAGGATTTATTTAAGATTGAGAAAACACGCATGACAAAATTTCTCTTAGATCAATACACTTTCAAGAAATGGAATAAGTCAGTGAATATTTTTTAAAACTGGCTAAACTGGACAGAATTGTGGGAGCAAGTCCCAAGGCATTTAAAAACAAATCTCGTGTAGCCAACTGTGTCAAAGGCAAAAAATAAATTACCATAAATTATATGGCCAAGGCAACTTAAAACAAAAACAGCTTGACGCCAAGGATTTCCTTAGCGCTTCCAGGAGTGTGTAACACTGCTTCTGGCCCTCAGGTCGGAGCAGCAACCGTCAGTCGGTGGGCCCCATAAGACCGCTGAGCTAGCGTCGGACACCACGGAGGAAATGGCTCCGTGGCTCGTCTGAGGTTCACTCCGCAGTCGTGTCCCTGGTAGGGAAGACCCATCTCGCGGGCTTATACACAAAGGGCAAGATACTGTTCGAATTCCGCCACCTCCCCTAGGAGCTCAGTGGGGCTGGGTTGGATTCCGTGCCATCCCGGCAGGTCGTGCCTCGGGAGGGGCGAAGGTTGCCCGGGGCTGGCGCTGGTGCTGCTGCTGCGGTGGCGGCGGCGGTGCCTGCGGTTGCAGCGGCTGCTGGGGATGCGCGTGGAAACCGCGCCCCGTCTTGCAGGCGGGCGAGCCCATCGCGCCGTAGTACAGGTGCATAGCGCTGGGGGCGCCAGGATCCCGGCGTCGCAGGGCCCGAGGGTCCGGCCCCACTGCGTGGACAGCGGGCGGCTCTACGGACACTGCATAGCCGGAGACTGGAGCGTAAGGTAGGTGCCGGCCGCCGGGCAAGCCTGGCAGCGGGGCTGCAGGAGCCGGAGCCTGCTCCACGCCATCCAGCGGGTATGTGTCCGGAGTGGGCAGAGTAGCCATCGAGCGCGGGAGCGCCCAGCCTGGCTAGCTCGATAGTGGCCCATGTGCGGAGACATCAGCGGGGACCGGCCGGATAGCCCGGCTCTGGAAAAGGCAGACCCAGGCCATCCATGGCCACGCGGCCGCCTCGGGACCAAGCGCGCCGGCCTGGGGCTCGACGAAGAGCGTGCAGGAAGCCTCCCTCCACCCGCTTCACGCTTCACCTGCCGCGCCGCCGCGGCCGGTACTTGTTGGGGTGGTCCTGCATTATGCTGCACGCGCAGCCGCTGGGCCTCTTCCACGAAGGGCCGCTTCTCTGCCAAAGCCAACGCCTTCCAAGACATGCCTAGCATCTTGCTTAGCTCTGCGTTGTGCCAGATCTGGGTTCTGCTGTGCCAACCGCTTGCGTTCGTCTTTGGCCCACACCATAAAGGCGTTCATCGGCCGCCGGA * NM:i:119 ms:i:1023 AS:i:978 nn:i:0 ts:A:+ tp:A:P cm:i:188 s1:i:958 s2:i:0 de:f:0.0673 cs:Z::45+t:39-g:3+tt:14-a:11-t*ga:5-g:12-ct:14-c:1*ac:14-ccct:7+g:4-g*ta:4-g:1-c:24+g:17*ac*ca:15*tc:24-a:33*ga*tg:1*ga:10-aat:3-gg:3*ag:1*tg*tc*gc:1*ac:3-gt:49+c:4-ga:44+cg:20+a:19-tgcggt:22+g:5+g:27*gt:1-a:1*at:9-g:21*ct:1-t:5-g:55*ta:22-c*at:5+a:35*gt:6-g:14-c:6*ag:13-g:15-c:2-at:1*gt:2*ca:29*tc:1*cg:16-t:20+a:2-tcc:17-aa:2-a*ag:6*ga*tg:23*gt:20-gg:6*ga:20-tc:6+t:2-t:1*ct:7-ggg:25-a:23*ct:2*ga:36-c:35+a:34-tg:12-t*tc:21-gta:17+t:21*cg:33*ga:1*tc:16*ta:3~ct431ac:28+c:77 rl:i:0 MM:Z:N-21891,66,59,64,261,29,68,47,271,53,16,6,209,38,51;N-17802,21,7,70,144,52,67,91,132,25,175,65,34,76,156; ML:B:C,5,254,5,3,253,98,15,254,217,72,12,121,243,9,46,2,11,3,10,41,160,134,187,7,11,22,20,94
4c718cef-9dbc-449e-b6b6-1ae47507d721 16 1 4774301 60 1S17M1I17M1D3M1D23M1I82M3D39M2D2M1I2M2D22M3008N2M2I29M1D12M3I34M1D16M1D3M1D9M3D12M4919N16M1I14M1D6M1I6M1I46M2D25M2D5M1D12M1I30M1217N38M8D46M1I19M1I25M1I7M1I12M1467N48M1D4M1I28M1I1M1I4M2D11M * 0 0TATAACAAAAGTTTCCCTCCTTACTTTAGAAATGGGTGTGGGGCAGATGCAGGCACACATGGAAGGCCAGATGCAGGCACACATGGAGACCAGATGCAGGCACACATGGAGGCCAGATGCTGGTCAGATGTCTTTTCTCAATGGCTTTATTATTTTATGTGTATTGAGTATCTGGCCGAAAGTCTGTGATCAAAAGAGTGCATCAAGTGCCCTGAAGACTTCTGGGGTCATAGAAGGCTGTAGTACAACACCGCCATTTTTTTTTTCAATGGCAGCAATGGCTAATTCTGAAGCAGCTGCACTTCAATATAATTTTGCTTGAGTATCAGCACCCTCTTCAACCAGCTGGAACTCCATAATCCCTTTAAGCAGGCTGGAATGGTCACACCTCTCCCATTCACAAGCTGGGTTAGGTCAATAGGTTGTTGGATCAACTCGACCTAAATCAAAAATATGTAGTCTCCTGAAGACTCAAAGGCTGATACTGGTGCCTGAAACTATGTCCTTCATTAAATCCATATTTTGGGATTCGTATGAGTCTGCCCTCCCTCAAAGCCTAGCCTTGGCCGGGTTCCTCTCTGCCCTTTCTCCTTTATGGCCTCCTGCCACACTTCCTACCTCTTCTCCTGATCTCTGAGGACGTCTTTCCCGTTTTCTTGAGTTAGGACTGGGCTTCAGGTTGGCCAGGCTCACTCTGGCAGAGGACCGCAGCAGGTCCAGGCTGGTCCCTGCCAGCCGCGCCGTGCC * NM:i:60 ms:i:595 AS:i:457 nn:i:0 ts:A:+ tp:A:P cm:i:103 s1:i:479 s2:i:83 de:f:0.0539 cs:Z::17+c:17-a:3-g:23+a:82-ttt:28*tg:7*ag:2-ca:2+t:2-ag:3*ga:18~ct3008ac:2+ga:8*tg:20-a:12+ttt:34-c:16-t:3-t:9-aaa:12~ct4919ac:16+a:14-c:6+a:6+a:46-ga:25-tg:1*ga:3-c:12+a:30~ct1217ac:38-gtaaaatg:22*ct:23+c:19+c:25+t:7+g*ta:11~ct1467ac:9*gt:38-c:4+g:28+t:1+c:4-cg:11 rl:i:14 MM:Z:N-21891,21,9,53,89,32,35,42,44,4,26,154,37,58,6,111;N-17802,42,96,12,215,176,44,46,45; ML:B:C,20,153,48,143,53,6,2,81,9,30,56,20,77,120,24,14,28,83,17,29,22,2,9
Hello @ADHDrian,
This has been a long-standing limitation but is easy enough to remove. I'll look into getting it into the next release. What caller is producing MM:Z:N-21891 tags?
Hello @ArtRand , thank you very much for your reply. It would be extremely helpful if you can indeed add this generic feature. The caller that produces these tags is not an official software release, but some research code that attempts mod base calling other than m6A and psi.
Hi @ArtRand
Happy new year. I have modbam files generated by DNAScent, which currently seem to be incompatible with modkit. I was wondering if it might be possible to consider accommodating this in the future. Thank you! Here is a read example
28b0c22d-5944-40b3-8272-2a14e7c7f0b5 16 chr1 260071 60 12600S8M1D7M2I10M1D28M1I18M2I2M1D34M3D8M4D8M3D61M3D77M1D9M3D25M1D7M1I6M1D66M1I1M1I25M1D8M1I15M2I11M1I6M2D18M1I1M2D11M1I23M1I5M1I20M1D26M2I10M1I23M1I33M1D8M1D12M1I19M1D22M2I44M1I36M1D146M1D2M1D8M3D12M1I7M1I4M1I3M1I21M1....
qs:f:8.61011 du:f:108.294 ns:i:541471 ts:i:10 mx:i:2 ch:i:1524 st:Z:2024-07-16T09:37:54.450+00:00 rn:i:7235 fn:Z:PBA01454_08d50ba0_4838ad5a_3.pod5 sm:f:730
.842 sd:f:125.658 sv:Z:pa dx:i:0 RG:Z:4838ad5ae9ec0013fd93f1e86510378a12d35db7_dna_r10.4.1_e8.2_400bps_fast@v5.0.0 NM:i:3313 ms:i:37813 AS:i:37172 nn:i:0 de:f:0.0938473 tp:A:P
cm:i:574 s1:i:7670 s2:i:6862 MD:Z:8^T8G8^G2T25C19^G4G2C26^CAG8^GGAG8^GTT0T0G31C25G1^GAT25A6T3T17T9G0A1T2A1T0C3^T9^CTG25^G13^G44T17T1T3T4T4T2T2G0A6^C35C4^CA19^GC13T4T2T19C2G14^A30C0T27T5T26^
G8^A31^G14G1C11T73^A10A80G54^C2^T5T2^GGG1C15A1G11G6C1G3C2^C1T0G2A0G16^G23C4^AT0A2T2^T67A9T15^C18T0G12^C29^C1^C6T0C2^G0C17^A8T0T16C10G1A2C3T1C2^A3^ACAA11^A2C9^T10^AAA1T16^C1^G0A6^A1^G5T2^T8^G0G3C2T4^T2A3^C3^CC
AACA2A0G0C3T3^AAC0A18^C20G26^ACC6C1C1C0T4^A3^G99G3C2^ACAG2^C0T15T5^GGT7^G6T5C8A13C0T1A1G3G8C0A16C7A0G4^CC0C7T19^GA2^AA4^C1G2^ACTA2^AC3^GAC2^TAAAT1T2G23^AG35^A15^A10C1G5C2C16^CA3T2T2^T8^AAA0T37A30G2^G3^AG4C3T1
18^T3^GA79T0G21^A9^GG7T13^G5^TC20^C2C1T0G57C11C0T3T0G4^C7^AG3^A9T2^G13A2A4C4G0T1A1T4G2^T5^T59G26C10C0T4^G41^A36A15^C34A2G41T0G38^AA4A0A1^G2C8^TT8C2^T64C7^A56T0C3G1^T0G2T4T0C13^TG0T37^G14^A17^T14^T3T9^A1T28^A9
C35T0G1T3T0C2T12T7^A13^T24^CT25^AA2^TA7^AAAAA1^G2G3C6C0G9^A48A19C2A4^G8^GC2A7G1^G3C2^T10C0T19T0G10^A21T23A4^T15G4^GA4^A55T0T4^C14^T5C0C2A10G6^T2^ATA17^CT13T1A1C35C4^T2G1^C7^C7^C9^C22^TA2T2T35^T18^C3G2C5G3C47A
0G0A2G77^T65A7^A11T0G25^A43A2^C74^AT1^T25A0C0T41^T5^T5^A8^C24^TA14C0T20G0C3C1^A2^C0C1C15T2^TAA2^C43^AAC1^C14^G63C15G2A2^C3T0C28C23C2C4^G2T19T0G4T2T2^T1A3^T11^A29^C5^C8T1A2C1G0A14C0T0G7T3G5^G16^T14^C4^ACT2^G71
C0T25A11C8C5T2^T7C2^C2A14^A0T3^T2T1C3C11^T54T32C14^TAGG12^G14T3T4^A28^C1T18^AT1^AC1T0T75^C20^C0T20G7^CT22T17^AGCTA1C6C1^G3C31^TT5G3C7^TGG3T7C13C0T20C4G1A0G7^C12^G4^AG8A0G6C0C7^G97A0C1C10G2^G4C0G13C63^TC20^G12
^T18A39C46^T3C15G19G3^C5^T14T4T6^A4T0G1^G0C9^A3T8C52^TC8C0A2T0G0G2^TA2C1C1^T19C11^G19C14^TTTATCA59T0A12^G7T34T0T5C10^T56^G2^C1C1G25^T15A1^ATATT1G50T1A0C2C0A2T0G32^CAA1T3T0C8^C5T17T5^GCA0A6^GTG3A2T25^C1C43T1G3
^G1^G18^G15T0G1^TGT1C6^GC6^ATG2^C1^C0G5^T2G1^C4^T9^G11^CC4G1^AG10C6^C2C1^TC18^T17^C59C20^C5G1A1G1C30C8G4T0C51^C44G4^GGGC5^C1^GAG2^T5C0C22^C10T0C48T0T9^G9^C3G2T19^G1^GG3^C4^T6^C12^A4C77^CT42G1^C7T1G4^A10^TC1T5
3C39^T4C16^T11^A150C0T0C28G5C5A14^AGG3C1T0G62^CC0C55^A6^C8T12^TC6^C20G0T21^G12^G38^CT3^T30^G5^C2A86^G2C0C18C0T23G0G2C0C0C35A1C25C0T5C0T3T2G1T3T6C3^GAT0A1A7C46C3G11^A2^AA2^CA1C0A1T6C32^C2C11^C3C5^TC25A7^G32^TC
11^C1C7^TC2T0A1C0C1T1^CA2T1G5^T3^AAT4G3C1C52^G37A29^T52G0T24G3C10^TG14G7T5^C7^CTG10^A7G0T28C23^CT27^A8^G4G14^C10C2C0T2T9^CT8^C2A27^C11T74C0C1C0T12^C16^A30T1C0T0G0T1T6G6A0G21C4^T13^CTGA2C46T0C15^G7^GG2C10^G8^T
16G8^ACT2C36^C5^C34G0C0T6C2^T4^TTC22^A6C3C5C1A1G2^T1^AA2T2T2^T50C5G1C15^A9^G3G6^C12A4C60A9G9G3T3G6^C1T11T0C0T24^G0A2C1^C0A38A9G6^CTC2^T18A0C6T14G1^C13C50G38^C22^C1^A0C6C7^CAGAAT1^C8^A31T30C4T1T17T28^G5T0C1C1C
3T3T9^A1C35A0G11^CT22T2T24C8T62^A1^CC1G49^AT6^AAT1T3^GA1C1C42^GC6C11^C11^T40^C23C10C6^A9^AAT8^A8^TC37^C38^G1C0C2^GT2^CT9^A3C0C28^A0A3C1C25^CT16^T9^GC36G0T1T6^A14G1G46T22G20^A20T34^A7C0T3T16G34T0C13G2^C6C29^A3
7G34^TG2^A14G0C0T13G0T15^C10^TTCTTTTCTTTTC6^C20C15T106^ACCT8A9^T23^TA1^T11^C1C31^G8A0T2T0T1^CA5^A4^CA0G26T4T1C56A0A0G0G0A3T0G2C32^A4^T11G3T5G14G1T26^A17C2T2T102G22^G62^C40^C0A4C0A10^GG2C5^CTTAA54^A41T2C3C30C1
5^C26^G10^AA7^G61^AA12G0G9C5T0C10^AG11^A15C2C44C48^A5^A4T13^CT23T17G13^G17C0T2^C2G6G0G1^CC56G5^GTAA2A1T13T8G0A3T1T1A2^TG1C0A1T8^AAAA3T3^T8^T8T1T0G8G0C12G10^G2G1T44^A4T4^C25G55T14^CT18^G26G0A85A1G0G2^TTTTG4G2C
3^A4^C43G1^G20A0G3^C1G0G0G0T1G3A1G17G0T2C0C22^TG0T1T0T33^A8G29^A36^C34^CTA10^A17C0T6A1C2A3^GCCAAC56^T56^G3A1T6^A5C55T4C9^CT16^T10^ACAT2^T7C0T2G1T3C5G4^T5C0T6G7^CAT3A0G6G0T5T2T12^T1A0T0G4C2C24C12^ATA1C1A2C1^A8
^T5C8^A41A5^A12^T30^T1G25^T6^AA0G4^T33C9A3T2^CTTC2T2^T16^G9G3C0C6^A4^C2C2^TGTG3C22G14A2T1C1^G10^TC34^G24^A20^A122^A4C6C36T1C0A41^A2T0G23G49C7C1A3T0G11^T14^T16G2G24^GT1^T10^TC0T6^TG12T15C1T14C3C1^A3C3C0T37C28C
1G5^T18C22^TG26C1T0C15C7^G1A25C0T4G0G1C2C1^A1^A0T1T1T1T8T35T3T2T3A22^T0A0A10T22^T11C4^G98^G12^T15A2G4C28^AGA2T0G5A0T26^A28^TG19^G39A0G29^GA5T52^G2^T3A43T22C5T5^T7C13T25C13T22A4T81^T9^T70C41G28G1C26T14G7T5^A2T
67T5C1T6^T2T7A0T1C11^A15C5^ACTTT13^A8C0T64^C43G2^C3G1^GG1G8^C1^GG16^C18^C38^C6^AT21G65A31T9^G15^T4A2^C1C1C1G2A2^A45^T4^G0T23C80A61^T44C2^T0A1T4^AAG24T1G29C49^C1^C0C1T1T3T4T3^TG4T71T32^AG8C0T1^A2^GG38A2C7^AGA1
5^A4^TAA8A10^A16^AT0T3A13^CATAA1A0C2A1^G29^A10T8C34^AAG19^G12T78A36^T15T2^AGA2T33^A55C0A67G35C78T3T7T0G7^A0G2^T13^A2G78^AAG0A3^C0C0A10C40T3T10^T27^T10A0G2^C1^C3C2^C29C1C12T9G1C17T12T17^GG36^A2C52^AA70^A10T40^
T0G0T2T2T7^AA10G10^CAC1^T87^T2^TC19C0T11G1T14^T2G89^G16^C23G10^C1A5T2G4C1G40^A68G1T22^G0G1G69C1^G20^CTC10^GT1T2^G7T21^T1^C7C41^AC15G3T8^G12G1T11^C5^TCTAT1T2A1^CCA31^G1^C20^T43T3G4A7^A8G26A7T16^C0T27T0G1T5^AC0
T22^A0G8^T1A18^CGG9^G0A31G2C13C1^AC15G24C15T6C3^T28C42^GC20G10C0G2C18T12^A18^C5G3C17C6^C1A20^C21G3C37C5T2G4^AA9T3A0T20G21^T20^G39^T9G15T38^A5C4T34T0G2C63^TG1^TC28^G4C20^G18C15^T26^GC35C14^TGT1A1^CCT50^G78^T1G
40^C5T23C1^AG41^C7G9C7C0T15T0C5T9C0T0A3^C5C21^T10C45^T60^GCAAAA7^A9C0T4^AG3^T0G0G3^T0G3C8G0G0C1^C0C0G9^A14C0A2G1T5^GA4^T39C13T1^C33^A9^G24^G5^G1C1^G4C0T52A0A4C27G9C3^A38^C1T5^C4^T45^A2C3C0T12T0C0A4G2T21^A3G0C
0G4^G37^AA4^T9^C2G1T1A1^G49C12T21^G0C6T3T3T5C5T0G13T1^T12G31C2A0G63^C2^C7A2^CCA1^A23C58G5^CT1A36C5T17C12C1C0T3G1C2^C1A16^TC10T0A6G1A0G30G7A6G3T5A5^C0T47C19C34^A6^C19^T19^T5^G1A9^C9^G24^TGGT1^ATA0A2A75^GA4C22^
C0A24C0T13C0T17^TTCTT49^T5^C15^T51^T13A25^G17G4T0G7G12G0T5C2G2^C2G2G3^GC30C0A1G33^A27^CAG2G14G35G21T15G0T4C2^T30A2^AA2^T0G30^A4^C37^G22T0C0T29^GC5^G10^A41^G0T17A6C1G2^A25^A28^T5T0G14^AG3^AGAAC42^C63^T8^C6^A25
T3^C8C1^G20^C0A1T2C0T1T5^CA9T0A7G2T3T2T42^TAT6^C2T2^A32T6C6T2^A2C1G3T50G32T0C5^T1G1^GC19^T3^TTCTC13^G1C1^C1C17C22^GC3^C2C0C24^CTG23T0G4C10^G3G2^A15^T4C8^A30^T2T18G6C59^A10^CTC23^A2A1C61G4G36G4G4^C0A21^G40C0A2
^C4T8G33^A7G10^AG12^G10C65^A15^GC4T4^G1C25C6^TC5^T1^T7^T4^C9^C5^C4G0T14^T3^T0T17^A35^G1T0C24A7C2^CAGG8C26C1C7T0G5C50A3C50T12^C2^T2^TTC21^TCT0T1T4T0G4^T2T0T34C3^CC11^T3^A1T47^C7A7^C5T0G1^AA9^G9^C15T3T28^A1T52^
A7C33C3A39^A21^T0G0G61T0G2T2T17C9T0G2^AGAGCT4C1T3^AAAAAA26^A8T0G3G9T0A2T4C20A16^T2T5G0A11^A1T62A0T1^CT1A3^AAC10C2C12^C0A2A2G43T2^C22T22G2G11^T18C0T3C44G33C0T3^C20^C1^CAA1T2T22^C18A0G1G6T0G29T0G3C3T4^TG0T49^G0
G3C26^CC0C3C1A0C4G28G5T36^AG2^TA0T2T2G10A5^A1T19^C8^AT40^A37T4^TA0A2T37^G7T1^C0G1A3^G2^C2G2G1A0T17^G1G14A0G45A56^GA45A1C7A21C4T1C20T32^C7C20^AA0A6A0A1T6^TCTC6T12T19G7T1C9T17^CA38T3T1A0G1C3C0C4G7T25^T2A3^T2T0T
6A7T2T61^A4C36G65G0A29A1G9T6C32C117C0T6C0G3C0A1T0A2^C8^GG14^GAA0T10^C61^G4^C0A18G24T23^G89^A4C21^G10G25^A41C49G1^G3^A10A21G0T1T3T3^TAA1^A7^CT18^AAAAA17^C15T0G12^AC0A13C58G1T65T2^TG2^G7^T13C72T79^A12T5^C9^CAA1
3C2^T1^GGGGAAAAAAAA3^C23^TGCA1^G12^TG8T4^T28T82^AAT22^A4C11^A16^T27^A22C4T12T0C40^G6G12C75T15T32G4^A2^GC0C7^A1T22A4^C8^GCTAAT37^T2^C11^G9G2C1C1C13 zd:i:2 rl:i:2479 SA:Z:chr4,190196696,+,30117S7642
M88D2923S,60,1619; MM:Z:N+b?,104,0,9,1,4,6,2,6,5,1,5,0,2,0,0,0,7,1,0,3,3,2,5,6,0,3,2,0,0,3,6,1,1,6,4,0,0,1,0,10,1,4,0,1,0,0,1,6,2,1,5,0,0,0,1,4,0,0,1,0,4,0,1,0,0,0,0,1,1,4,2,0,0,6,0,0,0,3,3,0,0,4,6,8,2,3
,1,0,3,2,0,0,3,0,0,0,5,3,2,6,0,2,0,2,7,0,0,2,1,3,2,0,0,1,2,4,0,1,2,4,1,0,4,0,2,1,0,0,4,0,8,6,0,0,1,2,0,1,1,0,1,3,4,13,2,2,1,1,1,0,1,2,4,6,2,4,1,4,1,3,3,2,1,0,0,0,4,9,0,4,0,5,9,2,2,0,5,2,0,1,3,1,0,7,2,2,4,3,2,
2,2,2,0,0,0,0,0,0,0,0,0,0,8,2,2,1,0,8,3,4,4,2,0,0,3,3,1,4,5,2,3,0,7,0,1,2,3,5,3,2,3,2,1,0,5,19,2,0,0,0,0,1,1,0,0,0,0,2,5,5,0,0,5,1,0,8,2,7,2,4,0,2,2,6,5,7,2,4,0,5,1,7,1,1,8,2,3,1,2,1,1,3,1,4,0,0,0,2,3,5,3,3,0
,0,2,2,3,0,8,3,6,1,1,0,0,0,0,4,0,6,3,2,6,0,0,5,0,0,0,1,0,0,0,0,3,0,0,0,1,0,0,0,3,0,0,5,0,7,4,3,1,9,0,2,1,5,2,0,2,9,0,5,2,6,2,0,1,1,0,0,0,1,1,0,0,1,1,0,3,0,0,1,5,6,4,9,1,1,1,0,0,1,0,1,0,0,1,1,0,2,3,0,1,2,2,0,0
,3,4,0,1,3,5,1,2,3,0,2,0,0,0,1,1,0,2,3,0,2,0,0,2,5,2,7,3,3,1,0,15,2,1,2,0,0,0,0,0,2,8,2,2,0,5,2,1,1,1,1,6,0,0,0,1,0,0,1,4,1,1,2,0,2,6,0,0,3,0,1,3,2,0,0,0,2,1,0,1,6,2,4,5,0,0,1,1,3,1,1,1,0,2,4,3,2,0,0,1,3,1,3,
1,1,4,2,3,0,2,3,4,2,3,1,2,0,0,0,3,1,0,0,6,3,0,0,2,0,7,2,0,4,2,0,0,16,1,1,5,0,3,0,0,0,1,3,4,3,4,1,1,3,0,0,0,0,3,0,0,0,0,3,2,3,1,0,2,3,2,1,4,3,2,1,2,0,1,2,0,0,0,2,0,0,3,0,0,1,1,2,2,3,2,2,4,0,0,0,0,0,0,0,0,1,1,1
,0,0,1,0,3,3,3,1,1,0,1,0,0,0,6,1,3,0,2,0,3,0,0,6,0,0,0,2,4,0,2,0,1,0,0,0,1,0,0,0,1,3,0,0,1,0,0,3,0,0,4,1,0,0,0,0,1,0,1,0,3,0,4,3,2,0,1,0,2,1,2,0,0,0,0,4,0,0,7,4,8,4,1,2,2,2,11,2,8,2,10,0,4,11,0,6,1,2,4,2,2,3,
1,10,1,2,6,13,2,8,1,3,1,10,1,2,0,0,3,1,3,3,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,0,3,1,1,6,2,0,0,1,2,0,0,3,0,9,2,6,1,3,4,2,4,2,2,0,1,1,1,1,0,0,0,0,1,3,1,1,1,1,1,0,0,0,0,4,2,0,0,0,0,1,1,0,3,1,2,2,1,0,1,0,3,1,3,1,0,0,1
,0,1,1,1,0,0,20,25,7,1,3,8,3,0,0,0,1,0,0,0,0,1,0,6,0,7,1,2,5,1,3,5,1,0,2,1,4,3,1,0,1,0,2,1,1,4,0,2,7,0,0,1,3,1,2,1,0,5,16,2,0,2,1,0,1,0,0,2,1,0,1,1,2,0,4,0,3,5,0,0,1,2,0,0,1,3,7,2,1,0,0,1,0,2,0,2,1,3,0,0,3,3,
2,2,3,0,0,1,0,2,2,2,0,1,1,2,1,0,5,1,4,0,1,4,1,1,9,0,0,4,1,4,1,1,5,2,4,16,0,0,7,2,2,1,3,3,0,0,5,1,3,1,2,0,1,1,2,2,1,0,0,3,8,10,0,4,3,3,3,3,0,3,0,7,3,0,5,0,0,1,1,3,0,12,2,2,0,1,6,2,0,1,3,1,2,0,5,3,1,0,2,1,0,0,0
,1,1,2,8,4,1,1,2,2,7,9,4,2,2,3,3,1,0,6,2,3,2,4,9,2,1,0,4,0,2,1,3,4,2,1,1,6,1,1,3,9,3,0,0,2,0,5,6,9,0,1,0,3,3,7,5,10,2,0,3,3,4,1,0,2,4,6,1,0,0,0,0,2,7,1,5,2,2,3,0,3,1,2,6,1,0,1,2,1,1,4,0,0,8,1,1,0,4,1,0,6,5,2,
3,4,2,0,0,1,1,2,1,7,1,1,5,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,13,4,4,4,2,7,3,4,11,0,4,2,4,4,2,2,4,2,2,1,0,3,8,4,4,0,0,0,6,0,0,0,0,10,0,0,0,4,1,0,3,5,2,4,3,4,0,5,1,7,5,7,0,0,0,1,0,3,0,1,0,1,9,2,12,2,3,0,5,1,1,3,
Thanks in advance!
Hello @KunFang93,
I can get this to you soon, it's on the roadmap.
Got it, thank you so much!
@KunFang93 Any chance you'd be willing to send me that fill SAM record so I can use it for testing? I can make one up, but better yet to test against teh actual output you have.
@KunFang93 Any chance you'd be willing to send me that fill SAM record so I can use it for testing? I can make one up, but better yet to test against teh actual output you have.
@ArtRand Sorry for the late response. For sure! I shared the files through dropbox to your email address. Please let me know if you don't get it. Thanks for your help!
Best, Kun
Hello @KunFang93,
I responded via email. Thank you for the sample data. I'll get you a build asap.
Hello @KunFang93,
I've sent you an email with some concerns I have regarding the output of DNAscent. Happy to follow up here or over email.
Hi @ArtRand
Thanks for your reply! Somehow I don't receive your email. Do you mind cc to kf2799[at]cumc.columbia.edu? Or go over here also works for me.
Best, Kun
@KunFang93
I'm glad I asked over here then! I've sent you email, let's correspond over there since it involves your data, and we can bring the discussing back public when necessary.