Multiqc: Report within BBMap tools request: pileup.sh

[magruca]

• Name of tool:
  
  
  
  • BBMap : pilup.sh
  
  
• Tool description:
  
  
  
  • This tool is a useful quick run of bp coverage/GC content/positive and negative strand coverage, etc.
  
  
• Tool homepage:
  
  
  
  • https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh
  
  
• File log output:
  
  
  
  • 41_DMSO_1.coverage.stats.txt
  
  
• Log filename pattern:
  
  
  
  • coverage.txt
  
  
• Most interesting data for General Stats table:
  
  
  
  • percentage coverage by chromosome (Covered_percent), GC content (Read_GC)
  
  
• Data suitable for MultiQC plot(s):
  
  
  
  • Histogram overlay of different features
  
  

Thanks for your consideration and efforts!

[ewels]

Hi @mgruca13,

Thanks for this! You've said that the filename pattern is coverage.txt, in that this tool always produces files called coverage.txt. But the example file you attached is called 41_DMSO_1.coverage.stats.txt.

Could you clarify what the output files from this tool are called please? I guess that there is no filename pattern - from the top of my head I think that's what BBMap usually does.

@boulund - here's another bbmap submodule for you if you have time 😉

Phil

[boulund]

Great fun!

I was quite hesitant to implement support for both pileup.sh and bbsplit.sh because they produce output for each reference sequence used, and the total volume can vary immensely. Imagine two small reference sequences -- no biggie, then all chromosomes of the human genome -- also not really an issue, but then someone (like me) comes along with reference gene catalogs of 10M sequences -- now the module needs to handle a wide variety of output visualizations for all these common scenarios. I just didn't have the time nor energy to come up with something general enough to handle these different sizes of output.

However, the work I'm planning to put into visualizing BBSplit output should be very easy to transfer to Pileup as well. Let's hope for the best 💃 I will probably complete both of these at the same time, whenever I can squeeze out the time required #757

[magruca]

Hi--

Sorry for any lack of clarity -- I know it was a pretty brief outline. You're right that there is no filename pattern so I just specified it. The basic output is just "coverage.txt". The file I attached is from one of the replicates I'm working on, thus the slightly different notation. I was trying different parameters of that tool and was just using the .stats to distinguish it from the runs.

I understand what you're saying about the gene catalogs -- it would be a similar issue to bedtools coverage depending on how that's run. I'll take a look at BBSplit, too, to get an idea of what you're talking about. I honestly just recently really started digging into BBtools, but in general they run so much quicker that I'm quickly becoming a convert.

Thanks again for the response and for looking into this! Let me know if you have any other questions.

Margaret

[boulund]

If you have any good ideas for how you would output from pileup.sh visualized in MultiQC I'd be very glad to hear them! Any inspiration you can provide is very useful, and will help give insight into how people typically use these tools. I'm also a BBTools convert--they're just very good all around. The unusual command line syntax took a bit getting used to, but it's really very flexible and I started to like it a lot, especially how paired/unpaired input/output files can be declared very conveniently.

Unfortunately I have a very limited amount of time to look into this for the foreseeable future, but it should be fairly straightforward to implement whatever we decide whenever I actually have the time to sit down with this. So keep bringing opinions/suggestions for how to handle this.

@ewels, what other MultiQC modules have solved similar challenges already?

[ewels]

I guess you could do a stacked barplot of those two statistics, one bar per sample, one category per chromosome. It'll be a lot of categories so pretty ugly, but should highlight any samples that don't follow the pattern.

It's probably worth allowing module config patterns to ignore chromosomes by name pattern and length (eg. skipping anything under 1 Mbp by default should keep things fairly clean).

Could even be clever and sum the total Length and only show chromosomes that make up at least x% (5%?) of the total, binning the rest into a single category.

[ewels]

Also, instead of a stacked barplot you could do a line plot with categories on the X axis for each chromosome. This would probably be better actually.

[boulund]

Sounds like a fun idea, I'll definitely play around with that.

[magruca]

I really like the idea of a line plot for each chromosome. Bar plots could
be used similar to what you use for RSeQC read_distribution, as well, with
100% being complete coverage. Then #bases could be used and have options of
total bases vs. percentages for the plot. That said I think a line plot
would probably be easier to visualize, especially if you are able to
incorporate GC reads.

In short I'm using pileup as a quick assessment to look at complexity in
conjunction currently with preseq. There is also a file that you can
produce using pileup that is a histogram which I have attached here. I'm
mostly working on nascent transcription analysis, so having GC content per
chromosome easily graphed would also be super interesting when addressing
GC bias -- how much is technical bias and how much is due to biological
reasons (e.g. TF binding sites). A quick way to look at this using MultiQC
over the large amount of data our lab is producing would be awesome.

Thanks again for snowballing ideas and taking the time to think about this!

On Wed, May 30, 2018 at 1:27 AM, Fredrik Boulund [e-mail]
wrote:

Sounds like a fun idea, I'll definitely play around with that.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/ewels/MultiQC/issues/768#issuecomment-393058276, or mute
the thread
https://github.com/notifications/unsubscribe-auth/Aj9fChOvHYNrlWA0-6nKNOOaS4mKbPwTks5t3knFgaJpZM4UOh5R
.

--
Margaret Gruca, M.A.
University of Colorado, Boulder
Jennie Smoly Caruthers Biotechnology Building (JSCBB), Dowell Lab
margaret.[email protected]

Coverage numBases

0 2995727882
1 40742817
2 21585264
3 13356609
4 8643419
5 5780407
6 3908369
7 2677227
8 1835395
9 1281172
10 908241
11 655668
12 484060
13 363204
14 279671
15 219978
16 178630
17 144845
18 121555
19 97696
20 84009
21 72594
22 62315
23 54344
24 46644
25 40988
26 34782
27 31301
28 29254
29 25500
30 22777
31 19601
32 18114
33 16167
34 15441
35 13630
36 13515
37 12098
38 10765
39 10454
40 10043
41 8664
42 8264
43 7786
44 7302
45 6566
46 6004
47 5732
48 5178
49 5499
50 4575
51 4449
52 4195
53 3944
54 3992
55 3891
56 3355
57 3311
58 3352
59 3016
60 2838
61 2853
62 2947
63 2640
64 2253
65 2276
66 2175
67 1701
68 1906
69 1862
70 1776
71 1830
72 1563
73 1898
74 1292
75 1459
76 1481
77 1433
78 1325
79 1365
80 1190
81 1169
82 879
83 1063
84 1098
85 1032
86 934
87 1019
88 1034
89 933
90 887
91 1013
92 932
93 889
94 896
95 780
96 890
97 814
98 808
99 685
100 619
101 716
102 798
103 754
104 656
105 841
106 776
107 680
108 622
109 573
110 780
111 656
112 566
113 534
114 592
115 693
116 513
117 572
118 547
119 590
120 530
121 459
122 581
123 671
124 502
125 462
126 458
127 529
128 460
129 494
130 528
131 367
132 391
133 479
134 537
135 441
136 340
137 455
138 394
139 365
140 351
141 312
142 287
143 439
144 281
145 261
146 278
147 327
148 199
149 349
150 351
151 330
152 277
153 278
154 262
155 346
156 295
157 257
158 250
159 255
160 316
161 250
162 297
163 444
164 328
165 269
166 248
167 269
168 263
169 229
170 246
171 276
172 234
173 207
174 223
175 213
176 262
177 280
178 267
179 263
180 286
181 221
182 207
183 167
184 203
185 237
186 210
187 181
188 192
189 171
190 192
191 180
192 182
193 220
194 240
195 171
196 240
197 196
198 175
199 156
200 258
201 146
202 137
203 160
204 171
205 184
206 164
207 214
208 244
209 205
210 177
211 153
212 183
213 143
214 135
215 144
216 152
217 130
218 142
219 159
220 170
221 158
222 182
223 262
224 134
225 142
226 158
227 161
228 169
229 204
230 141
231 161
232 155
233 165
234 165
235 154
236 149
237 141
238 129
239 146
240 222
241 124
242 174
243 192
244 164
245 110
246 158
247 132
248 104
249 115
250 145
251 124
252 103
253 107
254 137
255 147
256 129
257 139
258 172
259 171
260 160
261 113
262 161
263 167
264 175
265 143
266 153
267 196
268 144
269 168
270 141
271 151
272 122
273 167
274 133
275 126
276 125
277 140
278 131
279 160
280 168
281 193
282 120
283 198
284 154
285 151
286 147
287 134
288 133
289 120
290 138
291 166
292 158
293 124
294 195
295 186
296 147
297 121
298 155
299 131
300 139
301 125
302 114
303 118
304 115
305 106
306 109
307 112
308 116
309 113
310 112
311 117
312 120
313 91
314 112
315 110
316 132
317 107
318 104
319 111
320 118
321 159
322 93
323 91
324 95
325 113
326 108
327 122
328 96
329 124
330 135
331 85
332 117
333 118
334 167
335 168
336 114
337 93
338 88
339 99
340 192
341 145
342 95
343 79
344 124
345 141
346 101
347 79
348 104
349 90
350 75
351 133
352 94
353 84
354 76
355 78
356 76
357 58
358 69
359 92
360 74
361 76
362 67
363 122
364 54
365 76
366 79
367 70
368 93
369 67
370 77
371 103
372 69
373 76
374 69
375 62
376 60
377 104
378 85
379 62
380 128
381 87
382 63
383 156
384 76
385 112
386 57
387 113
388 85
389 72
390 75
391 93
392 78
393 78
394 76
395 66
396 67
397 71
398 70
399 65
400 80
401 108
402 58
403 56
404 80
405 67
406 68
407 68
408 64
409 63
410 70
411 142
412 69
413 53
414 56
415 96
416 72
417 51
418 60
419 45
420 50
421 58
422 52
423 49
424 43
425 76
426 61
427 51
428 57
429 50
430 57
431 58
432 56
433 141
434 47
435 57
436 64
437 65
438 57
439 78
440 57
441 67
442 65
443 64
444 64
445 107
446 60
447 84
448 51
449 63
450 73
451 70
452 109
453 51
454 61
455 57
456 66
457 59
458 65
459 63
460 42
461 49
462 89
463 50
464 46
465 50
466 44
467 47
468 51
469 45
470 58
471 61
472 51
473 53
474 52
475 62
476 37
477 38
478 38
479 42
480 42
481 39
482 38
483 48
484 37
485 60
486 59
487 44
488 38
489 45
490 54
491 46
492 43
493 52
494 61
495 55
496 55
497 68
498 32
499 33
500 44
501 37
502 33
503 49
504 52
505 68
506 43
507 60
508 46
509 48
510 43
511 42
512 44
513 57
514 33
515 27
516 32
517 73
518 102
519 55
520 47
521 39
522 38
523 35
524 116
525 115
526 49
527 44
528 52
529 49
530 36
531 54
532 45
533 53
534 47
535 62
536 70
537 30
538 46
539 51
540 64
541 55
542 49
543 54
544 49
545 62
546 51
547 41
548 59
549 41
550 47
551 54
552 42
553 40
554 45
555 31
556 31
557 35
558 41
559 49
560 37
561 44
562 48
563 34
564 34
565 45
566 46
567 41
568 46
569 38
570 42
571 44
572 40
573 25
574 43
575 29
576 44
577 39
578 55
579 46
580 60
581 35
582 30
583 35
584 29
585 30
586 24
587 49
588 42
589 48
590 41
591 30
592 48
593 43
594 29
595 40
596 26
597 38
598 37
599 43
600 25
601 41
602 39
603 33
604 38
605 42
606 46
607 38
608 29
609 30
610 36
611 38
612 38
613 38
614 34
615 30
616 32
617 30
618 30
619 29
620 49
621 37
622 32
623 37
624 31
625 31
626 36
627 29
628 31
629 32
630 56
631 43
632 67
633 33
634 59
635 35
636 38
637 73
638 27
639 35
640 26
641 23
642 37
643 33
644 38
645 37
646 40
647 37
648 39
649 47
650 70
651 32
652 33
653 27
654 27
655 44
656 92
657 32
658 28
659 37
660 37
661 35
662 34
663 33
664 45
665 70
666 42
667 76
668 27
669 32
670 38
671 59
672 59
673 75
674 35
675 41
676 19
677 32
678 38
679 41
680 29
681 35
682 35
683 39
684 40
685 27
686 29
687 23
688 37
689 28
690 22
691 51
692 32
693 29
694 28
695 32
696 29
697 27
698 45
699 31
700 82
701 50
702 27
703 24
704 23
705 32
706 29
707 20
708 12
709 32
710 30
711 36
712 23
713 27
714 24
715 24
716 39
717 32
718 45
719 19
720 33
721 24
722 23
723 26
724 27
725 32
726 24
727 31
728 32
729 22
730 21
731 32
732 26
733 19
734 26
735 24
736 73
737 26
738 52
739 22
740 41
741 26
742 27
743 19
744 22
745 22
746 28
747 22
748 25
749 32
750 25
751 20
752 24
753 31
754 24
755 22
756 31
757 29
758 22
759 33
760 58
761 41
762 39
763 26
764 40
765 32
766 20
767 38
768 21
769 14
770 20
771 34
772 33
773 24
774 29
775 29
776 27
777 26
778 29
779 26
780 31
781 30
782 28
783 38
784 29
785 29
786 24
787 43
788 20
789 31
790 30
791 19
792 22
793 27
794 33
795 32
796 34
797 35
798 32
799 27
800 23
801 23
802 30
803 38
804 26
805 30
806 26
807 31
808 36
809 32
810 32
811 34
812 39
813 33
814 27
815 27
816 40
817 41
818 35
819 40
820 35
821 40
822 31
823 34
824 33
825 25
826 33
827 33
828 26
829 32
830 27
831 39
832 33
833 31
834 32
835 35
836 36
837 25
838 29
839 31
840 26
841 28
842 28
843 39
844 24
845 87
846 33
847 35
848 35
849 35
850 46
851 29
852 39
853 63
854 30
855 24
856 19
857 25
858 31
859 28
860 30
861 26
862 34
863 26
864 23
865 26
866 21
867 38
868 24
869 34
870 22
871 21
872 20
873 31
874 34
875 22
876 28
877 31
878 33
879 27
880 24
881 22
882 24
883 31
884 25
885 30
886 21
887 23
888 20
889 28
890 20
891 26
892 18
893 11
894 28
895 24
896 26
897 20
898 21
899 28
900 22
901 23
902 22
903 26
904 19
905 22
906 26
907 20
908 21
909 19
910 16
911 12
912 16
913 18
914 14
915 21
916 21
917 15
918 18
919 20
920 23
921 17
922 11
923 27
924 21
925 11
926 27
927 24
928 22
929 14
930 27
931 20
932 17
933 23
934 9
935 20
936 21
937 31
938 20
939 22
940 21
941 13
942 20
943 13
944 13
945 18
946 15
947 11
948 12
949 16
950 17
951 21
952 20
953 17
954 16
955 21
956 17
957 26
958 29
959 22
960 25
961 17
962 23
963 19
964 16
965 28
966 16
967 18
968 28
969 25
970 21
971 17
972 28
973 28
974 16
975 24
976 18
977 13
978 21
979 15
980 24
981 18
982 24
983 16
984 26
985 18
986 35
987 10
988 23
989 20
990 18
991 18
992 26
993 20
994 20
995 31
996 23
997 24
998 25
999 26
1000 32
1001 20
1002 29
1003 19
1004 20
1005 12
1006 27
1007 27
1008 23
1009 30
1010 32
1011 36
1012 21
1013 24
1014 22
1015 18
1016 27
1017 23
1018 20
1019 21
1020 19
1021 14
1022 28
1023 17
1024 12
1025 24
1026 15
1027 23
1028 18
1029 24
1030 15
1031 19
1032 17
1033 17
1034 15
1035 14
1036 34
1037 28
1038 25
1039 19
1040 13
1041 16
1042 15
1043 12
1044 16
1045 11
1046 14
1047 33
1048 15
1049 18
1050 26
1051 19
1052 24
1053 27
1054 18
1055 18
1056 17
1057 18
1058 9
1059 19
1060 18
1061 19
1062 22
1063 16
1064 9
1065 14
1066 13
1067 16
1068 11
1069 16
1070 10
1071 16
1072 11
1073 14
1074 18
1075 17
1076 18
1077 12
1078 23
1079 15
1080 17
1081 12
1082 22
1083 11
1084 17
1085 7
1086 17
1087 15
1088 17
1089 15
1090 14
1091 7
1092 21
1093 19
1094 23
1095 12
1096 15
1097 15
1098 19
1099 14
1100 11
1101 15
1102 15
1103 14
1104 8
1105 10
1106 12
1107 12
1108 13
1109 10
1110 13
1111 9
1112 21
1113 19
1114 11
1115 19
1116 16
1117 17
1118 12
1119 15
1120 13
1121 13
1122 26
1123 16
1124 15
1125 17
1126 16
1127 19
1128 14
1129 20
1130 12
1131 8
1132 12
1133 17
1134 16
1135 14
1136 16
1137 13
1138 16
1139 17
1140 8
1141 20
1142 12
1143 15
1144 11
1145 9
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1147 9
1148 14
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1150 13
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1152 10
1153 11
1154 16
1155 17
1156 11
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1158 23
1159 15
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1164 14
1165 22
1166 14
1167 19
1168 14
1169 11
1170 17
1171 14
1172 10
1173 17
1174 15
1175 19
1176 10
1177 13
1178 23
1179 14
1180 13
1181 17
1182 10
1183 21
1184 17
1185 12
1186 16
1187 18
1188 21
1189 17
1190 12
1191 17
1192 16
1193 12
1194 18
1195 11
1196 15
1197 13
1198 15
1199 15
1200 18
1201 14
1202 18
1203 13
1204 23
1205 13
1206 20
1207 24
1208 20
1209 18
1210 15
1211 17
1212 15
1213 21
1214 14
1215 16
1216 17
1217 17
1218 14
1219 22
1220 12
1221 12
1222 24
1223 18
1224 11
1225 17
1226 16
1227 15
1228 15
1229 21
1230 21
1231 16
1232 18
1233 20
1234 23
1235 15
1236 28
1237 41
1238 20
1239 16
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1241 17
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1243 16
1244 14
1245 24
1246 14
1247 23
1248 15
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1250 14
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1255 21
1256 17
1257 19
1258 17
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1260 14
1261 16
1262 17
1263 21
1264 12
1265 15
1266 20
1267 10
1268 28
1269 12
1270 17
1271 13
1272 16
1273 15
1274 14
1275 18
1276 15
1277 16
1278 21
1279 14
1280 20
1281 9
1282 15
1283 15
1284 12
1285 25
1286 9
1287 22
1288 11
1289 12
1290 10
1291 15
1292 5
1293 14
1294 7
1295 10
1296 11
1297 9
1298 12
1299 14
1300 11
1301 13
1302 12
1303 12
1304 15
1305 12
1306 15
1307 3
1308 10
1309 14
1310 6
1311 9
1312 8
1313 10
1314 11
1315 8
1316 4
1317 13
1318 9
1319 12
1320 13
1321 7
1322 12
1323 9
1324 8
1325 8
1326 12
1327 7
1328 9
1329 9
1330 11
1331 13
1332 9
1333 9
1334 10
1335 8
1336 9
1337 13
1338 7
1339 10
1340 6
1341 10
1342 10
1343 18
1344 6
1345 13
1346 12
1347 10
1348 12
1349 10
1350 5
1351 11
1352 12
1353 8
1354 10
1355 15
1356 9
1357 10
1358 14
1359 10
1360 21
1361 18
1362 14
1363 6
1364 14
1365 13
1366 9
1367 13
1368 17
1369 14
1370 10
1371 20
1372 21
1373 12
1374 15
1375 11
1376 14
1377 12
1378 11
1379 18
1380 10
1381 16
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1385 6
1386 16
1387 24
1388 15
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1391 11
1392 15
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1397 7
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1401 16
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1403 25
1404 21
1405 12
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1407 7
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1413 13
1414 11
1415 19
1416 28
1417 20
1418 15
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1420 14
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1422 19
1423 16
1424 13
1425 14
1426 9
1427 10
1428 14
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1436 15
1437 12
1438 16
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[ewels]

Hi @mgruca13,

Thanks for the context - that's helpful! If you could attach the histogram data as a file through the GitHub web interface that would be great. I think it has been truncated here, plus GitHub can change the whitespace sometimes, so file uploads are always more reliable.

Cheers,

Phil

[boulund]

I think the coverage histogram (covhist) is actually already covered (edit: unintentional pun! 👍 ), see e.g. https://github.com/ewels/MultiQC/blob/master/multiqc/utils/search_patterns.yaml#L29
and https://github.com/ewels/MultiQC/blob/master/multiqc/modules/bbmap/bbmap_filetypes.py#L159

Since the file detection is done by content and not filename it should be able to find it already.

[magruca]

Got it -- just tried it out, thanks!

On Wed, May 30, 2018 at 8:58 AM, Fredrik Boulund [e-mail]
wrote:

I think the coverage histogram (covhist) is actually already covered: see
e.g. https://github.com/ewels/MultiQC/blob/master/multiqc/
utils/search_patterns.yaml#L29
and https://github.com/ewels/MultiQC/blob/master/multiqc/
modules/bbmap/bbmap_filetypes.py#L159

Since the file detection is done by content and not filename it should be
able to find it already.

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Jennie Smoly Caruthers Biotechnology Building (JSCBB), Dowell Lab
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[ewels]

@boulund - I found the module that does this coverage-per-chromosome plot already. It's samtools idxstats. I imagine you can use much of the code that's already there..

[boulund]

Super, thanks for doing that research! Does that already handle situations with up to tens of thousands of "chromosomes"?

[ewels]

Yup - it goes through the chromosomes one by one until it has represented 99.9% of reads (default, user configurable). It also has user-config keys for chromosomes to always show and always hide chromosomes, plus to define which chromosomes are X / Y for a sex prediction plot.

It's not the cleanest code ever, but it's functional 😉

https://github.com/ewels/MultiQC/blob/2d873203de31dbfe3ff0bfc3852c040937a4b212/multiqc/modules/samtools/idxstats.py#L36-L104

https://github.com/ewels/MultiQC/blob/2d873203de31dbfe3ff0bfc3852c040937a4b212/multiqc/modules/samtools/idxstats.py#L126-L145