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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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Coordination to DCC: bulk Atac-76 #211

Open twang15 opened 3 years ago

twang15 commented 3 years ago

Hi Ingrid and Jessica,

I am looking at the audit table (low FRIP score audit). And I came across https://www.encodeproject.org/experiments/ENCSR452OSK/

Which has some audits but is released. Is that on purpose?

Thanks, Annika

twang15 commented 3 years ago

Hi Annika,

From what I can recall, this was an experiment we ran and released before the newer ATAC-seq QC cutoffs were finalized by Anshul. Through previous slack conversations, I saw that it might have been possible to add more reads to these experiments, where most of these have about 20M reads. We also discussed these on a previous call to see whether rerunning them with auto detect would help.

After reprocessing, here are all the released ENC4 ATAC-seq experiments with not compliant audits on the portal: https://www.encodeproject.org/report/?type=Experiment&accession=ENCSR647AOY&accession=ENCSR846VPV&accession=ENCSR731ODJ&accession=ENCSR074WMH&accession=ENCSR452OSK&accession=ENCSR212LYK&field=%40id&field=aliases

Sorry about this. You don’t need to do anything if you don’t want to, but please let us know how you want this to be dealt with such as whether you can add more replicates, sequencing runs, etc.

Thanks and all the best,

Jessica Au Associate Data Wrangler ENCODE DCC

twang15 commented 3 years ago

Hi Annika,

Is there any update on this issue?

Thanks, Tao