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11 months ago
anii
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0
I have get this output by using mosdepth. It give me coverage at 1X, 5X,10X,15X ,20X , 30X. In some regions genes are repeated as you can see in the example. Can be merge the coverage of same genes or not? how Can i convert the coverage in the form of percentage?
example: ouput file from the mosdepth
chr start end region 1X 5X 10X
1 911555 911675 PERM1 120 120 120
1 911875 912027 PERM1 152 152 152
1 914248 915309 PERM1 1061 1061 1061
1 915409 916407 PERM1 998 998 998
1 916489 916609 PERM1 120 120 120
1 917425 917545 - 120 120 120
1 934423 934807 HES4 384 384 384
1 934900 935020 HES4 120 120 120
1 935058 935357 HES4 299 299 299
1 948894 949014 ISG15 120 120 120
1 949338 949888 ISG15 550 550 550
1 955565 955764 AGRN 199 199 199
1 957557 957841 AGRN 284 284 284
1 970615 970735 AGRN 120 120 120
1 976064 976265 AGRN 201 201 201
1 976539 977085 AGRN 546 546 546
1 977326 977532 AGRN 206 206 206
1 978615 979422 AGRN 807 807 807
1 979490 979633 AGRN 143 143 143
1 979690 979841 AGRN 151 151 151
1 980512 980663 AGRN 151 151 151
1 980758 980878 AGRN 120 120 120
1 981098 981243 AGRN 145 145 145
1 981339 981491 AGRN 152 152 152
1 981517 981667 AGRN 150 150 150
1 981748 982133 AGRN 385 385 385
1 982207 982354 AGRN 147 147 147
1 982684 982830 AGRN 146 146 146
1 982931 983078 AGRN 147 147 147
1 983156 983295 AGRN 139 139 139
1 983375 983757 AGRN 382 382 382
1 984226 984434 AGRN 208 208 208
1 984634 984838 AGRN 204 204 204
1 984908 985191 AGRN 283 283 283
1 985263 985415 AGRN 152 152 152
1 985585 985705 AGRN 120 120 120
1 985825 985945 AGRN 120 120 120
1 986075 986217 AGRN 142 142 142
1 986365 986485 AGRN 120 120 120
1 986604 986756 AGRN 152 152 152
1 986829 987040 AGRN 211 211 211
1 987096 987216 AGRN 120 120 120
1 987336 987456 AGRN 120 120 120
1 988805 988925 AGRN 120 120 120
1 989156 989362 AGRN 206 206 206
1 989823 989957 AGRN 134 134 134
1 990220 990360 AGRN 140 140 140
1 1007170 1007374 RNF223 204 204 204
1 1007426 1007971 RNF223 545 545 545
1 1018272 1018392 C1orf159 120 120 120
1 1019286 1019745 C1orf159 459 459 459
1 1019828 1019948 C1orf159 120 120 120
1 1021248 1021381 C1orf159 133 133 133
1 1022501 1022621 C1orf159 120 120 120
1 1022860 1022980 C1orf159 120 120 120
1 1025699 1025819 C1orf159 120 120 120
1 1026250 1026391 C1orf159 141 141 141
1 1026828 1026948 C1orf159 120 120 120
use a loop and run mosdepth for each gene.
Can you please explain the steps?
https://www.cyberciti.biz/faq/bash-for-loop/
have to apply the loop on the output file?