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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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Pre-generated Alu database #85

Closed drtconway closed 1 year ago

drtconway commented 1 year ago

Hi xTea,

Thanks for putting out a tool which produces good results!

Can I ask about the pre-built database? The Alu database has the file name hg38_AluJabc_copies_with_flank.fa but looking at the content, it appears that the Alu sequences are AluY[abc] sequences.

First, is there a reason for the inconsistent file naming?

Second, can you explain the reason the database contains just the AluY sequences and not the other classes of Alu? I assume there are good reasons, but I couldn't see them documented in the paper or the xTea documentation.

simoncchu commented 1 year ago

Those are AluY abc, as they are the major active ones.