Pulsar data management: Old reps for a WT control

[twang15]

Hi Tao, can you let me know if you find fastq files for those (very old) experiments? This was SREQ-97 and I am looking for either rep2 or rep3.

Rep1 has been submitted to the portal long time ago but has quality issues and I’d like to use one of the other replicates instead.

Thanks, Annika

Joan SK-N-SH 5 2 SK-N-SH batch 5 rep2 CB-86 P7 SREQ-97 Joan SK-N-SH 5 3 SK-N-SH batch 5 rep3 CB-86 P10 SREQ-97

[twang15]

Hi Annika,

We have raw data for SREQ-97. I am running a pipeline to extract all fastq files and will update you if they are there.

Best, Tao

[twang15]

Hi Annika,

Fastq files of Rep 2 and Rep 3 have been generated. Do you still want them?

Best, Tao

[twang15]

Thanks. The problematic control is this one:

https://www.encodeproject.org/experiments/ENCSR593IWN/

We should submit rep 2 as a new control and link it to the same experiments (4 in total) as the problematic one (that should be unlinked).

Let me know if this doesn’t make sense, Annika

[twang15]

Hi Annika,

Could you please let me know the ENC number for the 4 experiments?

Thanks, Tao

[twang15]

Hi Annika,

I found the 4 experiments have all been released and I have to asked Ingrid for permissions.

Best, Tao

[twang15]

I think they would first process the new control and see if it’s better.

[twang15]

Hi Ingrid,

Could you please process the following experiments? We may need to submit new wild-type control if the quality does not look proper.

Experiments with ENCSR593IWN as a control: ENCSR603TMB ENCSR641XWH ENCSR922RFY ENCSR969AIM

Thanks, Tao

[twang15]

Hi Ingrid,

The four experiments have been released, so I will not be able to add a new wild-type control experiment for them.

Also, if possible, I prefer to create a brand new wild-type experiment for the new replicate 2, because submission of a new replicate to an existing wild-type control experiment is not supported by Pulsar and it will takes much longer to do it manually.

Thanks, Tao

[twang15]

Another solution is to hold back rep1 of the current control https://www.encodeproject.org/experiments/ENCSR593IWN/

It sounds reasonable since rep1 does not satisfy the quality requirement, right?

-Tao

[twang15]

Hi Tao,

If I understand correctly, we are waiting for a new replicate for this wild type control to be submitted: ENCSR593IWN. If that is too difficult to do in Pulsar, you could submit the new replicate data to a new, separate experiment instead (and after processing, we would associate this new control dataset with the 4 TF experiments listed at the beginning of this thread). Have you already uploaded this new data to another dataset?

Thanks, Ingrid

[twang15]

Hi Ingrid,

You are right. I have manually submitted the new replicate to ENCSR593IWN. You may reprocess the four datasets now.

Please let me know if there is any issue.

Thanks, Tao

[twang15]

All 4 ChIPs have been processed and released.

ENCSR603TMB ENCSR641XWH ENCSR922RFY ENCSR969AIM