GRCh38 and chrEBV ...

[J. Seth Strattan PhD]

The GRC’s GRCh38 analysis set ("GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids”) includes the Epstein-Barr virus sequence (as chrEBV). Processing pipelines that use that assembly but do not explicitly filter out reads that map there might produce files that cannot be displayed as custom tracks because the chrEBV sequence is not in the browser’s genome database.

Have you considered adding chrEBV to the genome database or otherwise handling reads or features that map there?

Thank you,

Seth

J. Seth Strattan, PhD --- js...@stanford.edu --- www.encodeproject.org --- 650-725-4735

[Luvina Guruvadoo]

Hello Seth,

Thank you for your email. There has been some discussion about this topic in our group. We have not yet made a decision as to whether we will add chrEBV to our database, but it is under consideration. Thank you for bringing this to our attention.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Regards,

Luvina

--

Luvina Guruvadoo
UCSC Genome Browser
http://genome.ucsc.edu

--