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StanfordBioinformatics / pulsar_lims

A LIMS for ENCODE submitting labs.
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ENCODE data submission: RNA-seq data ALS paper #894

Closed twang15 closed 2 years ago

twang15 commented 2 years ago

Hello Tao,

We need to upload some RNA-seq data to ENCODE (bulk, no single cell), it should be straight-forward. This is from our lab (so no worries that the same thing happens as last time with Greenleaf's data) and was used in the ALS paper. I prepared the submission sheet here https://docs.google.com/spreadsheets/d/1SADAgiw5r9z2UVN7oybGhLwZD9ma77rrZRtqCtnEtcI/edit#gid=859466862 and tried my best to fill out everything but let me know if something is missing.

I linked cells to each other so once we are filling in ENC numbers, it should update the other tabs as well. We need to ask for read permission to the folder on SCG (/labs/mpsnyder/JCK_Sai/RNAseq/fastq/)

Let me know if you have questions and thanks for your help! Annika

twang15 commented 2 years ago

Hi Annika,

Here is the github issue tracker: https://github.com/StanfordBioinformatics/pulsar_lims/issues/894

I will take a look and work on it this week.

Best, Tao

twang15 commented 2 years ago

Hi Tao,

I just checked with my colleague. r0 is just where there was a technical failure and they were not able to match the paired read. The number of r0 reads is minimal. We should just exclude them from the submission and delete them from the file.

Thanks! Annika

twang15 commented 2 years ago

Hi Annika,

The submission has been done.

Best, Tao