diff --git a/docker/Dockerfile b/docker/Dockerfile index e7bac8a..9f2137a 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -8,6 +8,7 @@ RUN apt-get update \ curl \ python3.11-dev \ python3.11-full \ + procps \ && rm -rf /var/lib/apt/lists/* # Install Poetry diff --git a/longplexpy/multiqc_plugin/modules/lima_longplex/__init__.py b/longplexpy/multiqc_plugin/modules/lima_longplex/__init__.py index 5013a14..a4602d8 100644 --- a/longplexpy/multiqc_plugin/modules/lima_longplex/__init__.py +++ b/longplexpy/multiqc_plugin/modules/lima_longplex/__init__.py @@ -385,7 +385,7 @@ def __init__(self) -> None: }, } - self.general_stats_addcols(data=longplex_summary_metrics, headers=headers) + self.general_stats_addcols(longplex_summary_metrics, headers=headers) # Detailed Metrics ############################################################# @@ -454,8 +454,8 @@ def __init__(self) -> None: } keys: Dict[str, Dict[str, str]] = { - "i7_demuxed": {"name": "ZMWs with i7"}, "i7_and_i5_demuxed": {"name": "ZMWs with i5 and i7"}, + "i7_demuxed": {"name": "ZMWs with i7"}, "i5_demuxed": {"name": "ZMWs with i5"}, "failed_to_demux": {"name": "ZMWs without i5 or i7"}, } @@ -479,9 +479,9 @@ def __init__(self) -> None: well_data = [summed_count_metrics[pool].well_counts for pool in pools] well_keys: Dict[str, Dict[str, str]] = { - "P7": {"name": "ZMWs with i7"}, "P7+P5": {"name": "ZMWs with i5 and i7"}, "P5+P7": {"name": "ZMWs with i5 and i7"}, + "P7": {"name": "ZMWs with i7"}, "P5": {"name": "ZMWs with i5"}, } diff --git a/tests/data/demux_either_i7_i5/bc1003.lima.summary b/tests/data/demux_either_i7_i5/bc1003.lima.summary deleted file mode 100644 index 9fff7e3..0000000 --- a/tests/data/demux_either_i7_i5/bc1003.lima.summary +++ /dev/null @@ -1,24 +0,0 @@ -ZMWs input (A) : 903040 -ZMWs above all thresholds (B) : 701858 (77.72%) -ZMWs below any threshold (C) : 201182 (22.28%) - -ZMW marginals for (C): -Below min length : 1 (0.00%) -Below min score : 54634 (27.16%) -Below min end score : 0 (0.00%) -Below min passes : 0 (0.00%) -Below min score lead : 201174 (100.00%) -Below min ref span : 103661 (51.53%) -Without SMRTbell adapter : 0 (0.00%) - -ZMWs for (B): -With same pair : 701858 (100.00%) -Coefficient of correlation : 64.82% - -ZMWs for (A): -Allow diff pair : 903040 (100.00%) -Allow same pair : 903040 (100.00%) - -Reads for (B): -Above length : 701858 (100.00%) -Below length : 0 (0.00%) diff --git a/tests/data/demux_either_i7_i5/i7_5_bc1003.lima.counts b/tests/data/demux_either_i7_i5/i7_5_bc1003.lima.counts deleted file mode 100644 index 3f3ed1e..0000000 --- a/tests/data/demux_either_i7_i5/i7_5_bc1003.lima.counts +++ /dev/null @@ -1,17 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -0 0 seqwell_UDI3_A12_P7 seqwell_UDI3_A12_P7 92592 94 -1 1 seqwell_UDI3_B12_P7 seqwell_UDI3_B12_P7 86682 95 -2 2 seqwell_UDI3_C12_P7 seqwell_UDI3_C12_P7 77353 93 -3 3 seqwell_UDI3_D12_P7 seqwell_UDI3_D12_P7 74757 96 -4 4 seqwell_UDI3_E12_P7 seqwell_UDI3_E12_P7 12880 92 -5 5 seqwell_UDI3_F12_P7 seqwell_UDI3_F12_P7 39520 93 -6 6 seqwell_UDI3_G12_P7 seqwell_UDI3_G12_P7 81872 93 -7 7 seqwell_UDI3_H12_P7 seqwell_UDI3_H12_P7 49498 92 -8 8 seqwell_UDI3_A12_P5 seqwell_UDI3_A12_P5 16653 96 -9 9 seqwell_UDI3_B12_P5 seqwell_UDI3_B12_P5 27684 96 -10 10 seqwell_UDI3_C12_P5 seqwell_UDI3_C12_P5 25545 90 -11 11 seqwell_UDI3_D12_P5 seqwell_UDI3_D12_P5 17179 97 -12 12 seqwell_UDI3_E12_P5 seqwell_UDI3_E12_P5 7762 95 -13 13 seqwell_UDI3_F12_P5 seqwell_UDI3_F12_P5 17288 98 -14 14 seqwell_UDI3_G12_P5 seqwell_UDI3_G12_P5 42420 93 -15 15 seqwell_UDI3_H12_P5 seqwell_UDI3_H12_P5 32173 95 diff --git a/tests/data/demux_either_i7_i5/i7_5_bc1015.lima.counts b/tests/data/demux_either_i7_i5/i7_5_bc1015.lima.counts new file mode 100644 index 0000000..63c9200 --- /dev/null +++ b/tests/data/demux_either_i7_i5/i7_5_bc1015.lima.counts @@ -0,0 +1,49 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore +0 0 seqwell_UDI1_A01_P7 seqwell_UDI1_A01_P7 162 99 +1 1 seqwell_UDI1_B01_P7 seqwell_UDI1_B01_P7 174 98 +2 2 seqwell_UDI1_C01_P7 seqwell_UDI1_C01_P7 160 99 +3 3 seqwell_UDI1_D01_P7 seqwell_UDI1_D01_P7 178 98 +4 4 seqwell_UDI1_E01_P7 seqwell_UDI1_E01_P7 239 99 +5 5 seqwell_UDI1_F01_P7 seqwell_UDI1_F01_P7 44 99 +6 6 seqwell_UDI1_G01_P7 seqwell_UDI1_G01_P7 140 98 +7 7 seqwell_UDI1_H01_P7 seqwell_UDI1_H01_P7 246 99 +8 8 seqwell_UDI1_A02_P7 seqwell_UDI1_A02_P7 143 99 +9 9 seqwell_UDI1_B02_P7 seqwell_UDI1_B02_P7 126 99 +10 10 seqwell_UDI1_C02_P7 seqwell_UDI1_C02_P7 85 99 +11 11 seqwell_UDI1_D02_P7 seqwell_UDI1_D02_P7 138 99 +12 12 seqwell_UDI1_E02_P7 seqwell_UDI1_E02_P7 153 99 +13 13 seqwell_UDI1_F02_P7 seqwell_UDI1_F02_P7 39 99 +14 14 seqwell_UDI1_G02_P7 seqwell_UDI1_G02_P7 127 98 +15 15 seqwell_UDI1_H02_P7 seqwell_UDI1_H02_P7 131 98 +16 16 seqwell_UDI1_A03_P7 seqwell_UDI1_A03_P7 143 99 +17 17 seqwell_UDI1_B03_P7 seqwell_UDI1_B03_P7 153 98 +18 18 seqwell_UDI1_C03_P7 seqwell_UDI1_C03_P7 142 99 +19 19 seqwell_UDI1_D03_P7 seqwell_UDI1_D03_P7 121 99 +20 20 seqwell_UDI1_E03_P7 seqwell_UDI1_E03_P7 93 99 +21 21 seqwell_UDI1_F03_P7 seqwell_UDI1_F03_P7 50 99 +22 22 seqwell_UDI1_G03_P7 seqwell_UDI1_G03_P7 69 98 +23 23 seqwell_UDI1_H03_P7 seqwell_UDI1_H03_P7 157 99 +96 96 seqwell_UDI1_A01_P5 seqwell_UDI1_A01_P5 272 98 +97 97 seqwell_UDI1_B01_P5 seqwell_UDI1_B01_P5 149 98 +98 98 seqwell_UDI1_C01_P5 seqwell_UDI1_C01_P5 142 98 +99 99 seqwell_UDI1_D01_P5 seqwell_UDI1_D01_P5 61 98 +100 100 seqwell_UDI1_E01_P5 seqwell_UDI1_E01_P5 123 99 +101 101 seqwell_UDI1_F01_P5 seqwell_UDI1_F01_P5 68 99 +102 102 seqwell_UDI1_G01_P5 seqwell_UDI1_G01_P5 196 98 +103 103 seqwell_UDI1_H01_P5 seqwell_UDI1_H01_P5 171 98 +104 104 seqwell_UDI1_A02_P5 seqwell_UDI1_A02_P5 314 98 +105 105 seqwell_UDI1_B02_P5 seqwell_UDI1_B02_P5 134 98 +106 106 seqwell_UDI1_C02_P5 seqwell_UDI1_C02_P5 218 98 +107 107 seqwell_UDI1_D02_P5 seqwell_UDI1_D02_P5 105 98 +108 108 seqwell_UDI1_E02_P5 seqwell_UDI1_E02_P5 126 98 +109 109 seqwell_UDI1_F02_P5 seqwell_UDI1_F02_P5 45 99 +110 110 seqwell_UDI1_G02_P5 seqwell_UDI1_G02_P5 172 98 +111 111 seqwell_UDI1_H02_P5 seqwell_UDI1_H02_P5 94 99 +112 112 seqwell_UDI1_A03_P5 seqwell_UDI1_A03_P5 240 98 +113 113 seqwell_UDI1_B03_P5 seqwell_UDI1_B03_P5 116 97 +114 114 seqwell_UDI1_C03_P5 seqwell_UDI1_C03_P5 133 98 +115 115 seqwell_UDI1_D03_P5 seqwell_UDI1_D03_P5 125 98 +116 116 seqwell_UDI1_E03_P5 seqwell_UDI1_E03_P5 158 98 +117 117 seqwell_UDI1_F03_P5 seqwell_UDI1_F03_P5 31 99 +118 118 seqwell_UDI1_G03_P5 seqwell_UDI1_G03_P5 143 99 +119 119 seqwell_UDI1_H03_P5 seqwell_UDI1_H03_P5 90 99 diff --git a/tests/data/demux_either_i7_i5/i7_5_bc1015.lima.summary b/tests/data/demux_either_i7_i5/i7_5_bc1015.lima.summary new file mode 100644 index 0000000..bcaee83 --- /dev/null +++ b/tests/data/demux_either_i7_i5/i7_5_bc1015.lima.summary @@ -0,0 +1,24 @@ +ZMWs input (A) : 6881 +ZMWs above all thresholds (B) : 6639 (96.48%) +ZMWs below any threshold (C) : 242 (3.52%) + +ZMW marginals for (C): +Below min length : 0 (0.00%) +Below min score : 162 (66.94%) +Below min end score : 0 (0.00%) +Below min passes : 0 (0.00%) +Below min score lead : 242 (100.00%) +Below min ref span : 180 (74.38%) +Without SMRTbell adapter : 0 (0.00%) + +ZMWs for (B): +With same pair : 6639 (100.00%) +Coefficient of correlation : 43.34% + +ZMWs for (A): +Allow diff pair : 6881 (100.00%) +Allow same pair : 6881 (100.00%) + +Reads for (B): +Above length : 6639 (100.00%) +Below length : 0 (0.00%) diff --git a/tests/data/demux_either_i7_i5/seq102_bc1002.lima.counts b/tests/data/demux_either_i7_i5/seq102_bc1002.lima.counts deleted file mode 100644 index b533d23..0000000 --- a/tests/data/demux_either_i7_i5/seq102_bc1002.lima.counts +++ /dev/null @@ -1,49 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -24 24 seqwell_UDI1_A04_P7 seqwell_UDI1_A04_P7 34946 97 -25 25 seqwell_UDI1_B04_P7 seqwell_UDI1_B04_P7 35662 96 -26 26 seqwell_UDI1_C04_P7 seqwell_UDI1_C04_P7 31836 96 -27 27 seqwell_UDI1_D04_P7 seqwell_UDI1_D04_P7 30918 97 -28 28 seqwell_UDI1_E04_P7 seqwell_UDI1_E04_P7 43413 98 -29 29 seqwell_UDI1_F04_P7 seqwell_UDI1_F04_P7 20542 98 -30 30 seqwell_UDI1_G04_P7 seqwell_UDI1_G04_P7 28289 98 -31 31 seqwell_UDI1_H04_P7 seqwell_UDI1_H04_P7 22155 97 -32 32 seqwell_UDI1_A05_P7 seqwell_UDI1_A05_P7 18968 99 -33 33 seqwell_UDI1_B05_P7 seqwell_UDI1_B05_P7 31979 97 -34 34 seqwell_UDI1_C05_P7 seqwell_UDI1_C05_P7 33265 97 -35 35 seqwell_UDI1_D05_P7 seqwell_UDI1_D05_P7 18742 97 -36 36 seqwell_UDI1_E05_P7 seqwell_UDI1_E05_P7 36007 98 -37 37 seqwell_UDI1_F05_P7 seqwell_UDI1_F05_P7 18132 98 -38 38 seqwell_UDI1_G05_P7 seqwell_UDI1_G05_P7 37224 97 -39 39 seqwell_UDI1_H05_P7 seqwell_UDI1_H05_P7 20831 97 -40 40 seqwell_UDI1_A06_P7 seqwell_UDI1_A06_P7 39097 96 -41 41 seqwell_UDI1_B06_P7 seqwell_UDI1_B06_P7 38652 98 -42 42 seqwell_UDI1_C06_P7 seqwell_UDI1_C06_P7 39587 97 -43 43 seqwell_UDI1_D06_P7 seqwell_UDI1_D06_P7 36384 97 -44 44 seqwell_UDI1_E06_P7 seqwell_UDI1_E06_P7 57796 98 -45 45 seqwell_UDI1_F06_P7 seqwell_UDI1_F06_P7 13749 98 -46 46 seqwell_UDI1_G06_P7 seqwell_UDI1_G06_P7 49066 98 -47 47 seqwell_UDI1_H06_P7 seqwell_UDI1_H06_P7 27405 97 -120 120 seqwell_UDI1_A04_P5 seqwell_UDI1_A04_P5 24833 95 -121 121 seqwell_UDI1_B04_P5 seqwell_UDI1_B04_P5 20529 92 -122 122 seqwell_UDI1_C04_P5 seqwell_UDI1_C04_P5 22645 92 -123 123 seqwell_UDI1_D04_P5 seqwell_UDI1_D04_P5 24017 95 -124 124 seqwell_UDI1_E04_P5 seqwell_UDI1_E04_P5 24399 97 -125 125 seqwell_UDI1_F04_P5 seqwell_UDI1_F04_P5 18072 97 -126 126 seqwell_UDI1_G04_P5 seqwell_UDI1_G04_P5 29637 96 -127 127 seqwell_UDI1_H04_P5 seqwell_UDI1_H04_P5 23031 95 -128 128 seqwell_UDI1_A05_P5 seqwell_UDI1_A05_P5 23647 95 -129 129 seqwell_UDI1_B05_P5 seqwell_UDI1_B05_P5 19434 95 -130 130 seqwell_UDI1_C05_P5 seqwell_UDI1_C05_P5 20042 95 -131 131 seqwell_UDI1_D05_P5 seqwell_UDI1_D05_P5 31319 95 -132 132 seqwell_UDI1_E05_P5 seqwell_UDI1_E05_P5 26454 96 -133 133 seqwell_UDI1_F05_P5 seqwell_UDI1_F05_P5 15344 97 -134 134 seqwell_UDI1_G05_P5 seqwell_UDI1_G05_P5 26032 96 -135 135 seqwell_UDI1_H05_P5 seqwell_UDI1_H05_P5 9897 96 -136 136 seqwell_UDI1_A06_P5 seqwell_UDI1_A06_P5 26360 94 -137 137 seqwell_UDI1_B06_P5 seqwell_UDI1_B06_P5 29235 96 -138 138 seqwell_UDI1_C06_P5 seqwell_UDI1_C06_P5 27299 95 -139 139 seqwell_UDI1_D06_P5 seqwell_UDI1_D06_P5 20415 94 -140 140 seqwell_UDI1_E06_P5 seqwell_UDI1_E06_P5 30159 96 -141 141 seqwell_UDI1_F06_P5 seqwell_UDI1_F06_P5 19682 97 -142 142 seqwell_UDI1_G06_P5 seqwell_UDI1_G06_P5 35585 96 -143 143 seqwell_UDI1_H06_P5 seqwell_UDI1_H06_P5 15783 95 diff --git a/tests/data/demux_either_i7_i5/seq102_bc1002.lima.summary b/tests/data/demux_either_i7_i5/seq102_bc1002.lima.summary deleted file mode 100644 index 2e0f966..0000000 --- a/tests/data/demux_either_i7_i5/seq102_bc1002.lima.summary +++ /dev/null @@ -1,24 +0,0 @@ -ZMWs input (A) : 1653295 -ZMWs above all thresholds (B) : 1328495 (80.35%) -ZMWs below any threshold (C) : 324800 (19.65%) - -ZMW marginals for (C): -Below min length : 0 (0.00%) -Below min score : 128550 (39.58%) -Below min end score : 0 (0.00%) -Below min passes : 0 (0.00%) -Below min score lead : 324785 (100.00%) -Below min ref span : 183922 (56.63%) -Without SMRTbell adapter : 0 (0.00%) - -ZMWs for (B): -With same pair : 1328495 (100.00%) -Coefficient of correlation : 33.76% - -ZMWs for (A): -Allow diff pair : 1653295 (100.00%) -Allow same pair : 1653295 (100.00%) - -Reads for (B): -Above length : 1328495 (100.00%) -Below length : 0 (0.00%) diff --git a/tests/data/demux_i7_i5/bc1003.lima.summary b/tests/data/demux_i7_i5/bc1003.lima.summary deleted file mode 100644 index 132fb9e..0000000 --- a/tests/data/demux_i7_i5/bc1003.lima.summary +++ /dev/null @@ -1,26 +0,0 @@ -ZMWs input (A) : 1098305 -ZMWs above all thresholds (B) : 195265 (17.78%) -ZMWs below any threshold (C) : 903040 (82.22%) - -ZMW marginals for (C): -Below min length : 2 (0.00%) -Below min score : 95182 (10.54%) -Below min end score : 0 (0.00%) -Below min passes : 0 (0.00%) -Below min score lead : 201214 (22.28%) -Below min ref span : 102227 (11.32%) -Without SMRTbell adapter : 0 (0.00%) -Undesired hybrids : 33828 (3.75%) -Not direct neighbors : 901573 (99.84%) - -ZMWs for (B): -With different pair : 195265 (100.00%) -Coefficient of correlation : 52.07% - -ZMWs for (A): -Allow diff pair : 1098305 (100.00%) -Allow same pair : 1098305 (100.00%) - -Reads for (B): -Above length : 195265 (100.00%) -Below length : 0 (0.00%) diff --git a/tests/data/demux_i7_i5/i7_i5_bc1003.lima.counts b/tests/data/demux_i7_i5/i7_i5_bc1003.lima.counts deleted file mode 100644 index f9dd4df..0000000 --- a/tests/data/demux_i7_i5/i7_i5_bc1003.lima.counts +++ /dev/null @@ -1,9 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -0 1 seqwell_UDI3_A12_P5 seqwell_UDI3_A12_P7 33567 96 -2 3 seqwell_UDI3_B12_P5 seqwell_UDI3_B12_P7 42371 97 -4 5 seqwell_UDI3_C12_P5 seqwell_UDI3_C12_P7 29845 98 -6 7 seqwell_UDI3_D12_P5 seqwell_UDI3_D12_P7 28272 98 -8 9 seqwell_UDI3_E12_P5 seqwell_UDI3_E12_P7 5861 97 -10 11 seqwell_UDI3_F12_P5 seqwell_UDI3_F12_P7 6796 97 -12 13 seqwell_UDI3_G12_P5 seqwell_UDI3_G12_P7 33947 98 -14 15 seqwell_UDI3_H12_P5 seqwell_UDI3_H12_P7 14606 96 diff --git a/tests/data/demux_i7_i5/i7_i5_bc1015.lima.counts b/tests/data/demux_i7_i5/i7_i5_bc1015.lima.counts new file mode 100644 index 0000000..4bed5d8 --- /dev/null +++ b/tests/data/demux_i7_i5/i7_i5_bc1015.lima.counts @@ -0,0 +1,25 @@ +IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore +0 1 seqwell_UDI1_A01_P5 seqwell_UDI1_A01_P7 248 98 +2 3 seqwell_UDI1_A02_P5 seqwell_UDI1_A02_P7 243 99 +4 5 seqwell_UDI1_A03_P5 seqwell_UDI1_A03_P7 228 99 +24 25 seqwell_UDI1_B01_P5 seqwell_UDI1_B01_P7 206 99 +26 27 seqwell_UDI1_B02_P5 seqwell_UDI1_B02_P7 123 99 +28 29 seqwell_UDI1_B03_P5 seqwell_UDI1_B03_P7 139 99 +48 49 seqwell_UDI1_C01_P5 seqwell_UDI1_C01_P7 197 98 +50 51 seqwell_UDI1_C02_P5 seqwell_UDI1_C02_P7 192 99 +52 53 seqwell_UDI1_C03_P5 seqwell_UDI1_C03_P7 199 99 +72 73 seqwell_UDI1_D01_P5 seqwell_UDI1_D01_P7 111 98 +74 75 seqwell_UDI1_D02_P5 seqwell_UDI1_D02_P7 122 99 +76 77 seqwell_UDI1_D03_P5 seqwell_UDI1_D03_P7 155 99 +96 97 seqwell_UDI1_E01_P5 seqwell_UDI1_E01_P7 236 99 +98 99 seqwell_UDI1_E02_P5 seqwell_UDI1_E02_P7 193 99 +100 101 seqwell_UDI1_E03_P5 seqwell_UDI1_E03_P7 171 99 +120 121 seqwell_UDI1_F01_P5 seqwell_UDI1_F01_P7 40 99 +122 123 seqwell_UDI1_F02_P5 seqwell_UDI1_F02_P7 30 99 +124 125 seqwell_UDI1_F03_P5 seqwell_UDI1_F03_P7 38 99 +144 145 seqwell_UDI1_G01_P5 seqwell_UDI1_G01_P7 219 99 +146 147 seqwell_UDI1_G02_P5 seqwell_UDI1_G02_P7 179 99 +148 149 seqwell_UDI1_G03_P5 seqwell_UDI1_G03_P7 127 99 +168 169 seqwell_UDI1_H01_P5 seqwell_UDI1_H01_P7 283 99 +170 171 seqwell_UDI1_H02_P5 seqwell_UDI1_H02_P7 147 99 +172 173 seqwell_UDI1_H03_P5 seqwell_UDI1_H03_P7 221 99 diff --git a/tests/data/demux_i7_i5/i7_i5_bc1015.lima.summary b/tests/data/demux_i7_i5/i7_i5_bc1015.lima.summary new file mode 100644 index 0000000..bad7784 --- /dev/null +++ b/tests/data/demux_i7_i5/i7_i5_bc1015.lima.summary @@ -0,0 +1,26 @@ +ZMWs input (A) : 11014 +ZMWs above all thresholds (B) : 4047 (36.74%) +ZMWs below any threshold (C) : 6967 (63.26%) + +ZMW marginals for (C): +Below min length : 0 (0.00%) +Below min score : 189 (2.71%) +Below min end score : 0 (0.00%) +Below min passes : 0 (0.00%) +Below min score lead : 244 (3.50%) +Below min ref span : 179 (2.57%) +Without SMRTbell adapter : 0 (0.00%) +Undesired hybrids : 86 (1.23%) +Not direct neighbors : 6967 (100.00%) + +ZMWs for (B): +With different pair : 4047 (100.00%) +Coefficient of correlation : 39.47% + +ZMWs for (A): +Allow diff pair : 11014 (100.00%) +Allow same pair : 11014 (100.00%) + +Reads for (B): +Above length : 4047 (100.00%) +Below length : 0 (0.00%) diff --git a/tests/data/demux_i7_i5/seq102_bc1002.lima.counts b/tests/data/demux_i7_i5/seq102_bc1002.lima.counts deleted file mode 100644 index fa25dcb..0000000 --- a/tests/data/demux_i7_i5/seq102_bc1002.lima.counts +++ /dev/null @@ -1,25 +0,0 @@ -IdxFirst IdxCombined IdxFirstNamed IdxCombinedNamed Counts MeanScore -6 7 seqwell_UDI1_A04_P5 seqwell_UDI1_A04_P7 28343 96 -8 9 seqwell_UDI1_A05_P5 seqwell_UDI1_A05_P7 21409 98 -10 11 seqwell_UDI1_A06_P5 seqwell_UDI1_A06_P7 23143 98 -30 31 seqwell_UDI1_B04_P5 seqwell_UDI1_B04_P7 18258 98 -32 33 seqwell_UDI1_B05_P5 seqwell_UDI1_B05_P7 19731 98 -34 35 seqwell_UDI1_B06_P5 seqwell_UDI1_B06_P7 24871 98 -54 55 seqwell_UDI1_C04_P5 seqwell_UDI1_C04_P7 18994 98 -56 57 seqwell_UDI1_C05_P5 seqwell_UDI1_C05_P7 23379 98 -58 59 seqwell_UDI1_C06_P5 seqwell_UDI1_C06_P7 27411 98 -78 79 seqwell_UDI1_D04_P5 seqwell_UDI1_D04_P7 21361 98 -80 81 seqwell_UDI1_D05_P5 seqwell_UDI1_D05_P7 20082 98 -82 83 seqwell_UDI1_D06_P5 seqwell_UDI1_D06_P7 17834 98 -102 103 seqwell_UDI1_E04_P5 seqwell_UDI1_E04_P7 18657 98 -104 105 seqwell_UDI1_E05_P5 seqwell_UDI1_E05_P7 19095 98 -106 107 seqwell_UDI1_E06_P5 seqwell_UDI1_E06_P7 23216 98 -126 127 seqwell_UDI1_F04_P5 seqwell_UDI1_F04_P7 8453 98 -128 129 seqwell_UDI1_F05_P5 seqwell_UDI1_F05_P7 8362 98 -130 131 seqwell_UDI1_F06_P5 seqwell_UDI1_F06_P7 6580 98 -150 151 seqwell_UDI1_G04_P5 seqwell_UDI1_G04_P7 15752 98 -152 153 seqwell_UDI1_G05_P5 seqwell_UDI1_G05_P7 19963 98 -154 155 seqwell_UDI1_G06_P5 seqwell_UDI1_G06_P7 23642 98 -174 175 seqwell_UDI1_H04_P5 seqwell_UDI1_H04_P7 15534 98 -176 177 seqwell_UDI1_H05_P5 seqwell_UDI1_H05_P7 11126 98 -178 179 seqwell_UDI1_H06_P5 seqwell_UDI1_H06_P7 14636 98 diff --git a/tests/data/demux_i7_i5/seq102_bc1002.lima.summary b/tests/data/demux_i7_i5/seq102_bc1002.lima.summary deleted file mode 100644 index b05f8ad..0000000 --- a/tests/data/demux_i7_i5/seq102_bc1002.lima.summary +++ /dev/null @@ -1,26 +0,0 @@ -ZMWs input (A) : 2103127 -ZMWs above all thresholds (B) : 449832 (21.39%) -ZMWs below any threshold (C) : 1653295 (78.61%) - -ZMW marginals for (C): -Below min length : 0 (0.00%) -Below min score : 186243 (11.26%) -Below min end score : 0 (0.00%) -Below min passes : 0 (0.00%) -Below min score lead : 324532 (19.63%) -Below min ref span : 177575 (10.74%) -Without SMRTbell adapter : 0 (0.00%) -Undesired hybrids : 77327 (4.68%) -Not direct neighbors : 1651203 (99.87%) - -ZMWs for (B): -With different pair : 449832 (100.00%) -Coefficient of correlation : 30.12% - -ZMWs for (A): -Allow diff pair : 2103127 (100.00%) -Allow same pair : 2103127 (100.00%) - -Reads for (B): -Above length : 449832 (100.00%) -Below length : 0 (0.00%)