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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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ENCODE data submission: SREQ-459 #939

Closed twang15 closed 2 years ago

twang15 commented 2 years ago

Hi Tao,

I thought that we were done with ChIP submission but we still got one from seq center today. Here’s the breakdown (SREQ-459):

ZNF688: New replicates 3 and 4: L-12199 L-12200

Add to ENCSR682AAS as technical replicates and ask the DCC to reprocess with the 2 new replicates. If those look good, we can delete the old replicates. Otherwise we will reshuffle.

MBD1 New replicates 3 and 4: L-12201 L-12202

Add to ENCSR158BGH as technical replicates and ask the DCC to reprocess with the 2 new replicates. If those look good, we can delete the old replicates. Otherwise we will reshuffle.

MECOM New replicates 3 and 4: L-12203 L-12204 Add to ENCSR935UQL as technical replicates and ask the DCC to reprocess with the 2 new replicates. If those look good, we can delete the old replicates. Otherwise we will reshuffle.

ZNF177: New replicate 3. L-12198 Add to ENCSR677ROK as technical replicate for rep 1 and ask DCC to reprocess with the new replicate 3 and the old replicate 6 (ENCLB659OID).

Let me know if ou have questions, Annika

twang15 commented 2 years ago

Extract fastq files from base calls (*.bcl) w/ bcl2fastq

twang15 commented 2 years ago

cs-271: https://github.com/StanfordBioinformatics/pulsar_lims/issues/940 cs-206( cs-576): https://github.com/StanfordBioinformatics/pulsar_lims/issues/941 cs-205 (cs-578): https://github.com/StanfordBioinformatics/pulsar_lims/issues/942 cs-292 (cs-579): https://github.com/StanfordBioinformatics/pulsar_lims/issues/943

twang15 commented 2 years ago

Hi Annika,

I have been working on the submission of SREQ-459. The system has a long delay to index all the datasets.

After it finishes, I will check the submission quality and let you know if I need more inputs from you.

Best, Tao

twang15 commented 2 years ago

Yes, you did. I read this email first before I read those two.

The email I sent yesterday was all I need to finish our last ChIP submission. Now, they are done.

Best, Tao