Inserted genomic element in mammalian genomes

This is a toolkit to scan mammalian genomes for interesting insertions of genomic fragments

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1. I'll scan liftOver chain files (hg38 based) to find insertions in other genomes relative to human

2. To scan all insertions (across >50 mammalian genomes), run:
   ./src/getAssemblyInsertions.py <assembly>
   (assembly for example is mm10, rn6, bosTau8 etc.)

3. Output for a given assembly is a bed file with four fields, eg: in the file: output_examples/mm10.gapsInChains.bed

	chr5	178604087	178604087	196_SS_gap587_0_13
	chr7	154699597	154699710	152_DS_gap3018_113_99
	chr13	78498645	78498749	23_DS_gap22218_104_1451
	chr20	9824436	9824623	22_DS_gap8377_187_119

the 4'th field string read as: <chainID>_<gap-type>_<gap-number>_<ref_deleted>_<query_insertions>

* chain_ID		// *the ID of the liftOver chain (downloaded from UCSC genome browser) on which we found a gap when comparing the human genome (hg38) to a query genome*

* gap_type		// SS if there is insertion in the query genome and no deletion in the reference; DS is we have ref deletion and query insertion (i.e., Single - and doble sided gaps, respectively)

* ref_deleted		// size of chain-gap in the reference genome (i.e., gaps on the target species chain)

* query_insertions	// size of inserted bases in the target species

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Copyright

© Amir Marcovitz