Prevent overlapping repeats

[palakpsheth]

Any suggestions on how to prevent overlapping repeat units? for example i only want unique repeats that do not overlap or contain any other repeats

thanks!

[yangao07]

Can you give a brief specific example?

[palakpsheth]

@yangao07 apologies for the delay. Here is an example:

readName repN copyNum readLen start end consLen aveMatch fullLen subPos consSeq 0674db42-f074-4189-bb90-d7c75129499f rep0 5.1 10156 104 1019 179 100 0 117,296,475,654,828,1006 CTATGTGAAAACTTTTTGATTATGGGTAAAATTAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGGCACCATTAAAGAAAATATCATCTTCGGCGTGTCTTACGACGAGTACAGATACAGAAGCGTCATCAAAGCATGCCAACTAGAAGAGGTAAGAAA 0674db42-f074-4189-bb90-d7c75129499f rep1 3.7 10156 1013 1667 176 96.3 0 1025,1202,1375,1555 CAGAATGAAATTCTTCCACTGTGCTTAATTTTACCCATAATCAAAAAGTTTTCACATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTGTATCTGTACTCATCATGACACACGAAGATGATATTTTCTTTAATGGTGCCAGGCATAATCCAGGAAAACTGAGAA 0674db42-f074-4189-bb90-d7c75129499f rep2 3.5 10156 1673 2293 179 99.3 0 1686,1863,2042,2222 CTATGTGAAAACTTTTTGATTATGGGTAAAATTAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGGCACCATTAAAGAAAATATCATCTTCGGCGTGTCTTACGACGAGTACAGATACAGAAGCGTCATCAAAGCATGCCAACTAGAAGAGGTAAGAAA 0674db42-f074-4189-bb90-d7c75129499f rep3 5.4 10156 2287 3236 179 98.3 0 2296,2473,2638,2813,2991,3170 ATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTGTATCTGTACTCGTCGTAAGACACGCCGAAGATGATATTTTCTTTAATGGTGCCAGGCATAATCCAGGAAAACTGAGAACAGAATGAAATTCTTCCACTGTGCTTAATTTTACCCATAATCAAAAAGTTTTCAC 0674db42-f074-4189-bb90-d7c75129499f rep4 9.7 10156 2984 4133 112 99.9 0 3164,3276,3388,3500,3612,3724,3836,3948,4059 TTTTCACATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTGTATCTGTACTCGTCGTAAGATTACCCTCTGAAGGCTCCAGTTCTCCCATAATCAAAAAG 0674db42-f074-4189-bb90-d7c75129499f rep5 8.8 10156 4791 5772 112 93.3 0 4821,4929,5046,5154,5266,5377,5497,5607,5710 CATCAAAGCATGCCAACTAGAAGAGGTAAGAAACTATGTGAAAACTTTTTGATTATGGGAGAACTGGAGCCTTCAGAGGGTAATCTTACGACAAGAGTACAGGATACAGAAG 0674db42-f074-4189-bb90-d7c75129499f rep6 5.4 10156 5688 6639 179 97.6 0 5714,5882,6056,6235,6414,6593 CATCAAAGCATGCCAACTAGAAGAGGTAAGAAACTATGTGAAAACTTTTTGATTATGGGTAAAATTAAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGGCACCATTAAAGAAAATATCATCTTCGGCGTGTCTTACGACGAGTACAGATACAGAAGCGT 0674db42-f074-4189-bb90-d7c75129499f rep7 3.5 10156 6633 7251 179 98.7 0 6645,6823,7001,7179 CAGAATGAAATTCTTCCACTGTGCTTAATTTTACCCATAATCAAAAAGTTTTCACATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTGTATCTGTACTCGTCGTAAGACACGCCGAAGATGATATTTTCTTTAATGGTGCCAGGCATAATCCAGGAAAACTGAGAA 0674db42-f074-4189-bb90-d7c75129499f rep8 3.7 10156 7248 7924 180 98.9 0 7257,7440,7620,7799 GAGTACAGATACAGAAGCGTCATCAAAGCATGCCAACTAGAAGAGGTAAGAAACTATGTGAAAACTTTTTGATTATGGGTAAAATTAGAGCACAGTGGAAGAATTTCATTCTGTTCTCAGTTTTCCTGGATTATGCCTGGCACCATTAAAGAAAATATCATCTTCGGCGTGTCTTACGAC 0674db42-f074-4189-bb90-d7c75129499f rep9 5.1 10156 7918 8836 179 99.4 0 7927,8105,8285,8462,8641,8819 ATAGTTTCTTACCTCTTCTAGTTGGCATGCTTTGATGACGCTTCTGTATCTGTACTCGTCGTAAGACACGCCGAAGATGATATTTTCTTTAATGGTGCCAGGCATAATCCAGGAAAACTGAGAACAGAATGAAATTCTTCCACTGTGCTTAATTTTACCCATAATCAAAAAGTTTTCAC 0674db42-f074-4189-bb90-d7c75129499f rep10 9.5 10156 9023 10154 112 99.3 0 9202,9313,9425,9537,9649,9761,9873,9985,10096 GAGTACAGATACAGAAGCGTCATCAAAGCATGCCAACTAGAAGAGGTAAGAAACTATGTGAAAACTTTTTGATTATGGGAGAACTGGAGCCTTCAGAGGGTAATCTTACGAC

[yangao07]

I am not sure what you want exactly.
For this example, which part of the result do you need/not need?

[palakpsheth]

Hi @yangao07 if we look at rep0 rep1 and rep2, rep0 and rep2 have the same sequence and period length. rep1 starts inside the start-end range of rep0 and so breaksup the repeat between rep0 and rep2. What would be good to see is a mode that excludes any overlaps of start-end rep regions based on choosing the longest period length or most unit coverage.

The expected period for the above is 179

[yangao07]

-l/ --longest will only output the tandem repeat that covers the longest sequence. That may work for your case.