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visanuwan / cresil

CReSIL: Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences
MIT License
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How to prepare risk.bed file #11

Closed khugmat closed 1 year ago

khugmat commented 1 year ago

I'm trying to prepare rmsk.bed file, Im convert my RepeatMasker .out file to TAB-delimited file, its still not working, I make that file the same as yours in "simulated data". Here my rmsk.out file. Please, help me with that, thank you!

SW   perc perc perc  query     position in query              matching           repeat                 position in repeat

score div. del. ins. sequence begin end (left) repeat class/family begin end (left) ID

41    9.9  0.0  0.0  1               17       81 (56831543) + (TTTAGGG)n         Simple_repeat            1     65     (0)       1

337 16.8 9.6 1.8 1 124 315 (56831309) + rnd-5_family-10090 Unknown 411 593 (421) 2
298 12.0 2.0 0.0 1 327 376 (56831248) C rnd-3_family-136 Unknown (49) 230 180 3
672 14.3 0.0 0.0 1 395 513 (56831111) C rnd-1_family-79 Unknown (35) 160 42 4
759 12.5 41.7 0.0 1 589 636 (56830988) C rnd-1_family-79 Unknown (49) 230 163 5
32 4.6 2.1 2.1 1 637 683 (56830941) + (GGGTTTA)n Simple_repeat 1 47 (0) 6
759 18.3 0.0 0.0 1 684 844 (56830780) C rnd-1_family-79 Unknown (33) 162 2 5 959 16.5 0.0 0.5 1 841 1035 (56830589) C rnd-1_family-79 Unknown (1) 194 1 7 981 18.0 0.0 0.0 1 1032 1225 (56830399) C rnd-1_family-79 Unknown (1) 194 1 8
936 16.6 0.5 0.5 1 1222 1415 (56830209) C rnd-1_family-79 Unknown (1) 194 1 9 969 12.7 1.1 0.6 1 1412 1585 (56830039) C rnd-1_family-79 Unknown (1) 194 20 10
1076 14.4 0.0 0.0 1 1603 1796 (56829828) C rnd-1_family-79 Unknown (1) 194 1 11
907 18.1 0.5 0.0 1 1793 1985 (56829639) C rnd-1_family-79 Unknown (1) 194 1 12 945 17.5 0.0 0.0 1 1982 2175 (56829449) C rnd-1_family-79 Unknown (1) 194 1 13 1152 11.4 0.5 0.5 1 2172 2365 (56829259) C rnd-1_family-79 Unknown (1) 194 1 14
227 0.0 3.2 0.0 1 2358 2388 (56829236) + rnd-5_family-3830 Unknown 153 184 (132) 15 1006 15.0 0.5 1.0 1 2362 2556 (56829068) C rnd-1_family-79 Unknown (1) 194 1 16 1019 14.5 0.5 0.5 1 2553 2746 (56828878) C rnd-1_family-79 Unknown (1) 194 1 17
913 14.7 1.6 1.0 1 2743 2935 (56828689) C rnd-1_family-79 Unknown (1) 194 1 18 1025 14.1 1.0 0.5 1 2932 3124 (56828500) C rnd-1_family-79 Unknown (1) 194 1 19 1147 13.4 0.0 0.0 1 3121 3314 (56828310) C rnd-1_family-79 Unknown (1) 194 1 20
1076 12.0 0.0 0.0 1 3311 3485 (56828139) C rnd-1_family-79 Unknown (1) 194 20 21

khugmat commented 1 year ago

I found in previous issue that I need to prepare file like this(in UCSC site), it’s still not working 4BCAB377-FE2A-4353-B5FB-F32D66453283