Folder naming / additional level

[ghost]

We would like to submit a specific dataset including NGS sequences from a cohort of MSM pairs (source and recipient).
Is it possible to add a new level (5th) for the pair identification (source / recipient) or to replace the actual optional Level 4 ("replicate", not necessary for our cohort)
Level 1: Patient ID (anything, unique, required)
Level 2: Sample date (YYYYMMDD format, required)
Level 3: Compartment (anything, optional)
Level 4: Replicate (anything, optional)
+/-Level 5: Pair ID (for example: S3 for the Source of Pair #3 or R12 for the recipient of Pair #12...)

thx
Antoine

[spond]

Hi Antoine,

In general it is not possible to ensure that such a mapping is unique. For example the same patient could be a recipient for one pair, but a source for another pair. The Level attributes are meant to annotate something intrinsic to the run, and immutable. I would suggest that you implement the mapping of (patient ID - date) to pair S/R in post processing.

Sergei

[ghost]

thx Sergei
I am working on a subset of data provided by Ben's student through
octamonkey. I really like this pipeline.
Do you think it will be possible to include AM in addition to DRM (see
table S1 from Sara's paper enclosed)? and CI for DRM frequency?
Is it possible to obtain an UDS error estimate value?

I will be mostly in HC this week if you want to discuss this

Best
A

Dr Antoine Chaillon
Postdoctoral Researcher
Center For Aids Research (CFAR)
Division of Infectious Diseases,
UCSD & VA San Diego Healthcare System
Stein Clinical Research Building #325
University of California San Diego
9500 Gilman Drive
La Jolla CA, 92093-0679

On Mon, Dec 22, 2014 at 2:54 PM, Sergei Pond notifications@github.com
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