Updated ENSEMBL request

[cgreene]

Context

We received an email.

Problem or idea

A number of the histone genes have undergone revision and deconvolution in ENSEMBL recently. For example: http://www.ensembl.org/Homo_sapiens/Gene/Idhistory?db=core;g=ENSG00000286522;r=6:26031589-26032099;t=ENST00000621411

The refine.bio calls for these datasets do not contain any ENSEMBL gene IDs with such high numbers.

The experiments in question are: SRP127360

• Zhao et al Sci Rep 2018
• runs SRR6410607-SRR6410610 (colon) and SRR6410615-SRR6410618 (blood) that are total RNA SRP003672
• Yang et al Genome Biol 2011
• runs SRR067385-SRR067387 (H9) and SRR067391-SRR067393 (HeLa) that are polyA-

Solution or next step

We would either address this by updating the gene annotations package or by deciding that we are unable to do this at this time. Whenever we do next update, we would make sure to re-run this experiment.

[kurtwheeler]

I have good news and bad news.

Good news

All the samples from SRP003672 reprocessed successfully!!

Bad News

All the samples from SRP127360 timed out after 3 hours.