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TCGA MC3 BAMs failing workflows

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    Jason Cerrato

    Hi Sabrina,

    Thank you for writing in, and thank you for creating that list of sample IDs. This is incredibly helpful for investigation of the issue. I will flag this up with project managers of the TCGA workspaces and get back to you as soon as I hear more from them on the status of these .bam files.

    Kind regards,

    Jason

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    Jason Cerrato

    Hi Sabrina,

    Just to confirm, are these sample IDs distinct from the other list you've provided for investigation?

    Kind regards,

    Jason

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    Sabrina Camp

    Hi Jason,

    Thank you for looking at this issue. These are distinct IDs from the other list I sent. However, when I looked at this list sent in this thread I did notice some with a missing bam path entirely. It appears that when I was making the list that I sent regarding samples with no paths present at all, I did not include the samples that had an "NA" entry in the data model. 

    Here is a revised list of the samples that have paths in the data model, but they are broken/ lead to no where. This reduces the list from 209 to 157 when I remove the "NA" bam paths. 

    I will update the ticket I submitted with the newly discovered "NA" bam path sample ids. Hopefully this makes sense! I attached a picture of the two different missing path scenarios that led to this mistake.

     

    All the best,

    Sabrina

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    Jason Cerrato

    Hi Sabrina,

    Understood! Thank you for the explanation and revised list. I will keep an eye out for your next wave of sample IDs.

    Kind regards,

    Jason

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