WebSite - Charges

The Charges tab on the front page of the website lists the charges that have been incurred for the investigations the core is conducting.

Scope

You only see charges for investigation that you have access to.  PIs will therefore see charges for all of their investigations.  Post-docs and grad students will only see charges for their projects, not  for others in the lab unless they are part of the investigation.

Timing

After an initial break-in period, we will load charges fairly soon after the service has been provided. Charges may be before it has been decided whether the service is billable, i.e., whether a run or lane has failed or not.  This will be adjusted on an on-going basis until, or even after an invoice has been created.

What do we charge for?

The cores charge for quality assessments, making libraries, microarrays, sequencing, basic data processing (RLB), more advanced informatics, as well as CPU charges from the PGFI cluster.

What's in a charge?

The core, FGC or NGSC, is set depending on the PI's affiliation and the service, e.g., microarrays are always through FGC, but other services may be FGC or NGSC.

The invoice number is set once an invoice is prepared for billing.

The investigation should be clear as well as the Service code (what we did) and the service type.

A service is free if it was performed, but failed due to a problem with the sequencers or something we did wrong.

The % Billed is used to (1) handle the fractional charges from PGFI CPU usage, (2) split services between invoices.

The '$' is the list price.  '$/Item' is the charge after the Free and % Billed is considered. This is what you will be charged.

The Instance Key is the name of the thing that the service was performed on or with, e.g.,
FGC0396/1 for a lane in a sequencing run
7890/7890 for bioA of sample 7890

msrx_FGC0350_3_hg18_rd for aligning and loading data from FGC0350/3 to hg18.

The description will usually be fairly cryptic unless we edit it by hand.

Started On and Ended On are the dates over which the service was performed.

FAQ Sample Queue

Introduction 

The sample queue currently covers only the steps from sample drop off to sequencing.  It does not yet automatically handle resequencing, but we are working on that. There is a diagram of our process at the bottom of the page.

This queue contains samples for both the NGSC and the FGC cores. Due to the time it takes to compete the various steps and the amount of manual review required, we will only update the queue once or twice a day.

QC

Quality control involves performing at least an Agilent bioanalyzer run and a qubit run. Additional runs may be needed if these fail or give contradictory results.  We are evaluating the use of the Kapa system for QC but this is still preliminary and is only being applied to samples selectively.

We track the various evaluations in a spreadsheet, the upload values once all checks have been done and we are confident in the results.  Thus in many cases work is being done on a sample that may it be reflected in the queue.

This queue covers, RNA and DNA, libraries just being sequenced, as well as libraries that need to get resequenced due to bad sequencing results.

After the bioanalyzer step, you will receive an email indicating the results, but further processing may be going to refine the concentration.

After QC samples are either marked BAD and processed no further, or are marked GOOD and move to library prep, pooling, or ready for sequencing depending on the sample type.

Extraction
Extraction of RNA or DNA from cells is rare.  Any RNA or DNA extracted will become a new sample and move to the QC queue.

Library Prep

Library prep covers making libraries from RNA or genomic DNA. These are typically time-consuming process that take away or two to process 8 samples.

The libraries produced are new samples that move to the QC queue.  Usually a bioA is done immediately, so he QC is to get the precise molarities.

Microarrays

Microarrays are performed by the FGC core. These typically take about 2 to 3 three person-days to perform. Currently Agilent is having trouble with their manufacturing and is not shipping any arrays.

Pooling

Pooling covers the dilution and mixing steps necessary to sequence on or more libraries.  We are very careful with this step as it is essential to achieving maximum read counts and even distribution across all libraries in a pool.  We qubit the dilutions and redilute if necessary.  Entries in this stage represent individual libraries which will be pooled to take up just a lane or two, usually.

Waiting to be Sequenced

This queue is the set of pools or individual samples that are ready to go. When a sample or pool will be sequenced in more than one lane, the queue entry will indicate this.

Sequencing Now

These samples are in runs that are going on 'now'.  This include runs that are just finishing or have recently finished.  The end of a run may also be defined manually when a run is having trouble.

Recently Sequenced

Recently sequenced is just a list of the recent runs, in case you missed your sample going through the queue.

Outline of sample flow through the NGSC or FGC Cores.