ENCODE data submission: scAS File validation error

[twang15]

Hi Ingrid, Jennifer and Tao,

There are 4 scATAC experiments on the portal that are part of a multiome series that have file validations errors. Could you please let me know what happened here and how we can solve this?

Thanks, Annika

File validation error

ENCSR668XPI ENCSR435CGY ENCSR169BCG ENCSR628POB

[twang15]

I also found this experiment has a similar issue: https://www.encodeproject.org/experiments/ENCSR924ZXU/

[twang15]

SREQ-314: (auto submission) https://www.encodeproject.org/experiments/ENCSR668XPI https://pulsar-encode.herokuapp.com/atacseqs/316 https://www.encodeproject.org/experiments/ENCSR435CGY https://pulsar-encode.herokuapp.com/atacseqs/315 https://www.encodeproject.org/experiments/ENCSR169BCG https://pulsar-encode.herokuapp.com/atacseqs/299

SREQ-308: (manual submission) https://www.encodeproject.org/experiments/ENCSR628POB https://pulsar-encode.herokuapp.com/atacseqs/298

[twang15]

It looks like that the files with validation error are different from others. In their names, they all have 'trim', e.g., /workdir/encode_scatac_dcc_2/results/ENCSR628POB-1/fastqs/R1_trim.fastq.gz

[twang15]

Hi Annika,

The problematic files are not submitted by us (looks like Anshul’s lab) You can see they have very different file names, e.g.,

/workdir/encode_scatac_dcc_2/results/ENCSR668XPI-1/fastqs/R1_trim.fastq.gz

-Tao

[twang15]

Hi Annika and Tao,

Tao is correct, these files are part of the processing submitted by Anshul, and the flag is due to no error on your part. These filtered FASTQs have some unexpected structure to their read naming that we will be patching the read_name_details property to account for, once all the snATAC processed data files are submitted to the portal.

Thanks for flagging this up, and let me know if you have any other questions/concerns about the snATAC datasets!

Best, Ingrid