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Published 20 hours ago • verified publisher icon mdcao

VNTR.xaf

Open sarah872 opened this issue 5 years ago • 4 comments

Where can I find this file?

sarah872 avatar Jul 01 '19 11:07 sarah872

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

Devika1 avatar Jul 04 '19 00:07 Devika1

Hi @Devika1

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

yunfeiguo avatar Oct 03 '19 18:10 yunfeiguo

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

Devika1 avatar Oct 04 '19 01:10 Devika1

Great, thanks!

yunfeiguo avatar Oct 05 '19 04:10 yunfeiguo