mdcao / japsa

Just Another JAva Package for Sequence Analysis

BSD 3-Clause "New" or "Revised" License

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VNTR.xaf #30

Open sarah872 opened 5 years ago

sarah872 commented 5 years ago

Where can I find this file?

Devika1 commented 5 years ago

You need to create this file with the information on the repeats you want to test. It requires Target ID, chromosome, start position, end position, size of the region, period, repeat unit, left flank size, right flank size, genomic coordinates of the target region including the flanking and the sequence of the repeat unit.

example:

ID chrom start end period unitNo size lflank rflank target repeatUnit

chr22_16059465_16059496 chr22 16059465 16059496 14 2.2 31 1000 1000 chr22:16058465-16060496 AATGCCTGTACCAC

yunfeiguo commented 4 years ago

Hi @Devika1

Could you explain what period, unitNo, size, lflank, rflank and repeatUnit in more details? Thanks!

Devika1 commented 4 years ago

Period - length of repeat unit unitNo - number of copies of the rpeat unit reported in reference genome size - length of the repeat sequence in reference genome lflank and rflank - size of flanking sequence to include in the analysis repeatUnit - sequence of the repeatUnit

yunfeiguo commented 4 years ago

Great, thanks!