intron_clusters_perind_numers.counts.gz looks odd.

[Saikat Bandyopadhyay]

I have generated the cluster counts with the leafcutter using the default parameters provided in the tutorial (https://davidaknowles.github.io/leafcutter/articles/Usage.html). However, the cluster counts that I get look strange as for some clusters the values are continiously zero across all of the samples. Additionally, the cluster counts seems to be varying drrastically across the samples. I am attaching a snapshot of the counts file

1:4774516:4776410:clu_1_- 0 0 0 0 17 6 1 0 0 0 0 5 0 0 0 11 8 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 2 0 0 0 0 0 0 0 0 0 3 0 2 9 1 0 0 0 0 0 0 0 0 0 0 0 1 0 4 2 8 0 0 19 7 0 0 5 2 2 0 2 0 0 1 0 0 3 0 0 0 0 0 0 0 0 10 0 0 0 0 0 14 0 0 0 0 0 0 0 0 0 0 5 0 0 2 2 0 0 4 1 0 11 0 0 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 0 0 13 0 0 0 0 0 0 4 0 0 0 3 0 6 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 0 0 5 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 0 0 3 2 0 0 0 0 4 2 9 0 13 0 0 0 0 0 25 5 4 0 0 0 0 0 0 13 0 0 0 10 0 0 0 0 1 0 0 0 8 0 6 0 0 0 0 0 9 0 0 0 0 2 6 0 0 0 0 0 8 0 2 0 0 4 8 12 0 0 61:4774516:4777525:clu_1_- 2 21 0 3 52 13 5 20 0 3 0 10 0 0 18 12 15 11 0 0 0 0 0 4 8 0 0 6 0 11 0 0 0 0 0 23 0 0 0 0 11 23 14 2 5 0 6 0 29 0 8 6 0 8 16 5 9 4 23 8 16 19 0 7 9 8 20 7 0 19 0 0 20 4 0 0 15 0 0 5 0 6 14 2 0 0 25 4 0 0 5 22 22 8 26 0 0 16 13 5 9 21 0 0 0 0 0 0 8 9 0 14 38 21 0 20 12 0 14 0 0 0 0 0 0 22 2 0 0 11 3 30 6 8 4 32 28 11 0 2 4 0 0 12 0 10 0 0 17 0 0 0 13 7 2 0 23 18 9 0 3 0 0 14 13 0 0 11 0 3 14 17 0 11 11 0 0 0 2 8 5 0 0 0 9 4 11 0 0 0 0 0 16 0 18 0 0 7 0 0 32 13 6 0 0 0 0 0 0 23 4 0 14 0 11 0 7 5 0 0 0 2 0 3 0 0 16 10 0 4 4 0 20 0 24 0 0 0 0 0 0 0 0 9 0 0 6 8 15 0 0 0 7 0 0 0 0 15 0 0 13 2 0 0 0 23 0 0 0 0 11 2 0 0 12 5 11 0 0 10 0 21 5 9 0 0 0 12 15 0 7 0 18 0 0 0 0 28 0 10 17 0 7 8 5 0 0 0 10 5 2 11 11 2 31 0 9 8 26 7 15 0 8 0 0 0 0 17 0 3 18 19 15 10 0 0 9 15 18 0 19 0 6 0 2 0 9 0 11 17 0 0 0 24 3 4 6 0 0 0 12 19 19 3 0 19 21 17 0 0 401:4776801:4777525:clu_1_- 213 521 0 128 362 196 108 193 0 84 0 154 0 0 229 154 224 232 0 0 0 0 0 101 107 0 0 83 0 198 0 0 0 0 0 320 0 0 0 0 68 249 175 44 72 0 64 0 247 0 106 117 0 68 271 113 142 96 485 115 228 107 0 187 105 116 162 65 0 169 0 0 219 72 0 0 139 0 0 90 0 93 159 85 0 0 254 123 0 0 78 101 173 117 110 0 0 214 118 82 96 200 0 0 0 0 9 0 96 111 0 150 162 214 0 150 108 0 93 0 0 0 0 0 2 252 148 0 0 151 69 243 102 75 145 204 424 146 0 51 124 0 0 179 2 63 0 0 84 0 0 0 239 186 126 0 210 178 131 0 155 0 2 157 113 0 0 175 0 115 158 151 4 62 235 2 228 0 78 105 181 0 0 0 191 141 132 0 0 0 0 0 354 0 292 0 0 109 0 0 273 125 47 0 0 83 0 0 4 183 181 0 110 0 147 0 102 126 0 0 0 206 0 142 0 4 95 276 0 131 76 0 163 0 249 0 0 0 4 0 0 2 0 105 0 0 127 163 98 0 0 0 140 0 0 0 0 362 0 0 219 0 0 0 0 182 0 0 0 0 129 141 2 2 214 76 129 0 0 121 0 270 65 167 0 4 0 90 94 0 68 0 230 3 0 0 0 185 0 208 415 0 135 184 199 0 0 0 95 46 129 83 277 106 285 0 88 63 369 130 292 0 157 0 0 0 2 375 2 97 126 272 107 110 0 0 112 172 190 0 133 0 119 0 46 0 121 0 190 49 0 0 0 188 83 96 85 0 2 0 128 114 300 147 0 172 222 302 0 2 2101:4777648:4778748:clu_2_- 0 0 0 0 10 0 0 0 0 0 0 2 0 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 2 0 18 0 0 0 0 5 0 3 0 0 0 0 0 0 0 3 0 0 0 0 0 1 0 0 3 2 0 0 1 2 0 0 0 6 19 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 10 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 2 2 0 0 7 0 0 6 0 0 0 0 0 0 0 0 0 0 0 0 10 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 0 0 0 0 0 0 0 2 0 0 0 0 2 0 0 0 0 2 0 0 0 0 14 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 10 0 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 1 2 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 7 0 0 0 4 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 1 0 0 0 0 01:4777648:4782568:clu_2_- 215 475 0 147 412 219 82 125 0 113 0 196 0 0 225 163 226 215 0 0 0 0 0 96 97 0 0 75 0 240 0 0 2 0 0 326 0 2 0 0 75 273 209 64 91 0 73 0 219 1 91 172 2 89 340 135 181 100 398 100 193 126 0 168 107 84 197 55 0 167 0 0 259 82 0 0 176 0 0 105 0 102 200 104 0 0 279 165 0 0 93 119 190 174 101 0 0 239 142 92 87 217 0 0 0 2 4 0 111 127 0 151 219 201 0 147 118 0 112 0 0 0 0 3 0 257 169 0 0 131 80 198 117 76 162 215 369 191 0 82 206 0 0 201 0 77 0 0 93 0 0 0 207 217 171 0 265 197 152 0 182 0 0 160 122 0 0 205 0 122 171 178 2 69 226 0 210 0 101 111 217 0 0 0 172 150 181 0 0 0 0 0 366 0 324 0 0 92 0 2 279 153 70 0 0 68 0 2 0 202 184 0 153 0 177 0 120 111 2 0 0 177 3 160 4 2 99 237 0 152 98 0 124 6 288 0 0 0 0 0 0 0 0 132 0 0 112 204 93 0 0 0 145 0 0 0 0 323 0 0 276 2 0 0 2 191 2 0 0 0 136 156 3 0 214 64 163 0 0 125 0 321 77 194 0 0 2 95 125 0 79 0 267 2 0 0 0 165 0 296 381 0 188 180 186 0 0 0 103 54 128 160 331 108 350 0 84 68 381 138 326 0 195 0 3 0 0 402 0 92 124 275 112 156 0 0 126 239 172 0 199 0 169 0 71 5 81 0 220 46 2 0 0 223 105 93 87 0 0 0 180 128 302 150 0 194 243 337 0 0 2291:4782301:4782568:clu_2_- 13 22 0 15 40 0 7 14 0 11 0 11 0 0 13 7 16 16 0 0 0 0 0 0 5 0 0 10 0 23 0 0 0 0 0 0 0 0 0 0 5 34 15 9 9 0 16 0 23 0 0 6 0 7 28 16 0 0 31 13 0 20 0 12 11 3 15 1 0 65 0 0 32 1 0 0 25 0 0 6 0 9 10 12 0 0 48 0 0 0 6 13 16 28 12 0 0 25 13 7 0 11 0 0 0 0 0 0 7 0 0 8 17 21 0 6 6 0 11 0 0 0 0 0 0 28 18 0 0 10 19 12 18 0 18 0 40 9 0 5 21 0 0 0 0 9 0 0 7 0 0 0 26 26 16 0 0 13 16 0 9 0 0 11 8 0 0 13 0 0 18 19 0 4 22 0 12 0 12 0 8 0 0 0 0 0 0 0 0 0 0 0 17 0 34 0 0 9 0 0 25 7 7 0 0 3 0 0 0 10 18 0 0 0 0 0 8 0 0 0 0 21 0 14 0 0 16 11 0 5 11 0 12 0 22 0 0 0 0 0 0 0 0 11 0 0 6 30 13 0 0 0 8 0 0 0 0 30 0 0 0 0 0 0 0 29 0 0 0 0 14 28 0 0 12 0 0 0 0 15 0 24 8 5 0 0 0 0 20 0 9 0 28 0 0 0 0 9 0 63 29 0 13 0 0 0 0 0 11 15 0 6 22 19 27 0 9 0 22 13 27 0 16 0 0 0 0 32 0 5 3 30 0 0 0 0 0 20 10 0 33 0 0 0 10 0 4 0 9 9 0 0 0 11 16 12 8 0 0 0 12 13 28 0 0 14 8 28 0 0 291:4782733:4783951:clu_3_- 229 445 0 142 438 173 78 220 6 107 0 155 0 0 204 156 209 229 0 1 0 2 0 104 116 0 7 88 0 207 4 0 4 0 0 309 4 10 0 0 89 294 178 92 117 0 131 0 227 4 153 100 8 91 350 154 181 70 274 103 240 122 0 171 110 100 215 68 10 213 0 0 228 80 2 0 231 0 0 126 0 114 202 122 0 0 369 149 2 5 66 101 209 148 129 0 0 238 126 90 138 199 0 2 2 0 0 0 146 110 0 149 189 222 0 155 124 0 114 0 6 0 5 0 0 261 188 0 0 200 70 257 133 107 108 232 364 190 9 72 196 2 0 209 0 89 0 0 58 0 4 0 240 222 151 2 207 162 140 0 166 0 2 153 135 2 0 198 0 130 162 111 0 47 216 0 200 2 88 163 252 0 0 0 210 152 148 0 0 0 0 0 364 2 298 0 0 135 0 0 363 154 71 0 0 55 23 0 0 190 195 2 87 0 166 4 118 148 0 4 0 179 8 197 2 2 119 268 0 183 90 0 170 2 260 0 0 0 0 0 0 2 0 107 0 0 115 217 120 0 0 0 125 0 10 0 8 336 0 2 239 0 2 0 0 204 0 0 0 0 122 198 4 0 185 80 121 0 0 136 0 298 61 188 4 4 2 108 163 0 99 4 184 0 0 0 0 155 0 316 380 0 154 188 171 0 2 0 109 74 103 108 324 110 273 0 102 99 365 153 307 0 155 2 0 0 0 329 0 96 138 275 131 180 0 0 106 248 140 0 284 0 140 0 108 2 112 2 238 70 0 0 0 199 138 86 101 0 4 0 202 160 312 187 0 159 294 269 0 0 2141:4782733:4784078:clu_3_- 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 12 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 14 0 0 0 0 0 0 0 0 0

I apologize for my rather naivate regarding this, but I will be greatful if you can kindly adress this.