FAQ

FAQ

Please see our Guidelines for our Core policy. Below are the questions we are most commonly asked.

What is the best way to contact us?

For general inquiry, please contact IHGSeqcore@ucsf.edu.

For bioinformatics questions, please contact IHGBioinformatics@ucsf.edu.

In-person meetings can be arranged by appointment.
(It’s best to not stop by our office/lab without an appointment, as it may cause confusion or interrupt the flow of work of our staff. Thank you.)

What is the best way to download our data from the IHG web-portal?

Sequencing data are often large in size and stored in multiple files, so we highly suggest avoiding VPN and WiFi connection.

Using Ethernet cable to connect to the UCSF network is a reliable way to download data. Also, your workstation/laptop may not have enough space to store the data. You should consider using an external hard-drive (1 TB or more) with USB 3.1 connection. If you are unsure about the best way to download your data, please feel free to discuss with us.

Do I have to use the command-line tool to download the data from the IHG web-portal?

No, you don’t have to use wget. You can use any software that supports recursive download via https. However, we won’t be able to provide any technical support if you choose to use any software other than our recommended tool.

What kinds of results do I get at the end of my project?

For most projects, you will have access to sequencing data in fastq format. For 10X projects, you will also have access to the output data produced by 10X software – we strongly encourage you to familiarize yourself with 10X software pipeline on the 10X website.

What is assay data re-processing?

Assay data re-processing is an umbrella term we use to describe any data re-generation only involved with computation. For example, rerunning bcl to fastq conversion is considered as assay data re-processing.

Why does it take so long to have my assay data re-processed / re-analyzed?

While we are trying to fulfill every request in a timely manner, we don’t have a dedicated team and computing resources to handle re-processing and troubleshooting. Therefore, we might not be able to work on your request right away, as our day-to-day operation has higher priority. You should consult with our staff if you are concerned about the turnaround time but you should be prepared for any possible delays.

The most common reason for data re-processing requests is providing the wrong index in the request form so please make sure you double check before submitting it to us.

How often do I get updates on my project?

Since we are a high-throughput core, we do not provide any status update on your project. We will let you know when the data is ready for downloading. While we are happy to provide an update upon request, doing so will distract us from working on your project, so please ask responsibly.

Why can't I get BCL files for my samples if I share the flowcell with other users?

Since we don’t separate our samples by lanes, there is no way we can isolate the sequences of your samples from the other samples. Therefore, we are unable to provide BCL files of your samples.

What kinds of custom analysis are available?

In general, if the scope of the project is limited and clearly defined, our bioinformaticians might be able to help depending on the timeframe, workload, and domain knowledge However, if the project is exploratory in nature, it is less likely we have the expertise and capacity to help. Our Core is staffed with experienced specialists running clinical exome sequencing. Therefore, we can accept requests for clinical genomic variants interpretation.

Please feel free to discuss your project with us to see if we can help.

What is the sample requirement and turnaround time for whole exome sequencing? Single-cell RNAseq? Ready-to-sequence libraries?

For whole exome sequencing, we request for high-quality DNA in 60ul at 20ng/ul (1.2ug total DNA).  We highly recommend using the Qubit or Picogreen for quantitation. If your DNA samples are extracted from FFPE, please let us know so we can process them accordingly. The typical turnaround time is 3-4 weeks depending on the sequencing queue and core workload.

For single-cell RNAseq on the 10x platform, we request for 50ul at 1,000 cells/ul in 1X PBS with 0.04% BSA on ice. Please do a cell and viability count prior to sample drop-off. The recommended cell viability cutoff is 70%. Please email us at least one week before your experiment to schedule the run and reserve wells on the 10x chip. The typical sample drop-off time is by 2pm on the day of the run. Kindly let us know if you are running late. Last minute cancellations or late submissions are subject to late fees. The typical turnaround time is 4-6 weeks depending on the sequencing queue and core workload. The wait time is much shorter if you just need the fastq files. If you need the Cell Ranger output files, there is a 1-2 week additional wait time.

For ready to sequence libraries, we request for 20ul at a minimum of 15nM. Please send Bioanalyzer traces along with the sequencing request form.

Where do we drop off the samples?

We are located at:

513 Parnassus Avenue, HSW 901A

Can I get my samples back after they are run?

We only keep the samples for one year. If you want to keep them, please contact us to schedule a time for pickup.

Disclaimer: The policies outlined in this document are intended as guidelines only and are subject to change without prior notice at the sole discretion of UCSF IHG Genomics Core.