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0xTCG / biser

A fast tool for detecting and decomposing segmental duplications in genome assemblies
MIT License
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BEDPE fields in output #8

Closed saraebell closed 2 years ago

saraebell commented 2 years ago

First, thank you for creating an easy to use tool for detecting segmental duplications.

I have successfully generated results using the BISER tool, but I noticed the output BEDPE file does not include the Field names when it is generated (neither does the elem.txt). Is there a way for the Field names to be included when generating the output BEDPE file? Thank you!

First 3 lines of output BEDPE file

chr1    3042602 3044990 chr1    45613987    45616318    mm9:mm9 6.4 +   +   1091    1102    4M1162S1102N141M2I113M9I35M138S138N690M13D39M1D55M  X=4.1;ID=2.3
chr1    3135187 3137396 chr1    28229835    28232644    mm9:mm9 19.5    +   +   985 986 249M24I137S161N26M119S119N12M90S91N13M113S113N5M43I442S481N112M88I37S1I286S3I363N284M1D125M X=3.2;ID=16.2
chr1    5099409 5104076 chr1    5100098 5104638 mm9:mm9 37.5    +   +   4667    5590    42M113D37M1I114M1I23M1I32M1I56M1I81M1I57M171I30M1I26M1I32M1I56M1I56M1I80M1I258M1I110M1D58M1D56M1D56M1D57M1D112M1D24M1D32M1D56M1D21M57D35M1D227M1I114M1I134M113D66M1I165M172D203M1D56M1I56M1D56M1I257M1D48M113D38M286D79M456I90M1D172M284I22M55D207M114I6M7I24M  X=2.3;ID=35.3
inumanag commented 2 years ago

Hi @saraebell

The name field is there: it is mm9:mm9 in this example and it is used to indicate reference genomes (typically genome:genome if you run BISER on a single genome). Let me know if this is not what you had in mind.