Merge the same gene and get percentage of gene from the output file of mosdepth tool
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15 months ago
anii • 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
mosdepth • 707 views
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use a loop and run mosdepth for each gene.

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Can you please explain the steps?

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have to apply the loop on the output file?

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