Analysis

Frequently Asked Questions

  1. When and where is the Q&A session?

Our Q&A sessions are every Thursday, from 2:00-4:00pm (NA 2.226). If this time is not convenient for you, please contact us and we will set a meeting that better fits your schedule. Please do so ahead of time so we can be prepared for our meeting. If we are doing analysis for your data, please make it a priority to discuss as many details about your experiment with us as you can. Not every experiment follows general guidelines for analysis and we are confident that with more understanding of your research, we will be able to help you reach your goals.

  1. What are the default genome versions supported by the Bioinformatics Lab?

The following should give you an idea of what our bioinformatics pipeline has been configured to. Of course these can be changed as per the researcher’s needs. Please contact us for individual inquiries.

Species

Experiment

Genome version

Provider

Human

Whole exome/genome

b37

Broad/NCBI

Human

RNA-Seq/ChIP-Seq

hg19

UCSC

Mouse

Whole exome/genome

GRCm38

NCBI

Mouse

RNA-Seq/ChIP-Seq

mm10

UCSC

Rat

RNA-Seq/ChIP-Seq

rn5

UCSC

Fly

Whole genome/RNA-Seq/ChIP-Seq

dm3

UCSC

Zebrafish

RNA-Seq/ChIP-Seq

danRer7

UCSC

Neurospora

Whole genome

NC12

Broad

Yeast

RNA-Seq/ChIP-Seq

sacCer3

UCSC

 

  1. Can the lab do analysis using a custom genome or a user provided genome?

Yes we can. Please contact us for individual inquiries.

  1. How much does the lab charge for data analysis?

Data QC mapping, and basic analysis is free of charge if it is generated in the McDermott Sequencing core and within the scope of our standard pipeline. If custom analysis is needed, we can negotiate on a per sample, per project, hourly or collaborative basis depending on your needs.

  1. What is the time estimate for bioinformatics analysis once the sequencing is complete?

If the data only needs basic analysis, please allow up to 2 weeks. We try not to rush the data as they need to go through a rigorous QC benchmark. If you are under a time crunch, please contact us and we will try our best to expedite the processing.

  1. Once we get the official e-mail from the lab regarding completion of analysis, where and how do we get the data?

If you are part of the UTSW network, the data can be downloaded/viewed from the link that we send you. Also, you can take a hard drive with enough capacity to NB 10.206 and have the data copied for you.

  1. How can we access data if we are not part of the UTSW system, or in a different location than the lab?

In such cases, either an FTP link can be provided or a hard drive can be shipped to your location.

  1. How long is the link active and your data stored in the McDermott center?

Your data and links are stored for one month in our storage. It is imperative that you copy the data during this time. We will send out an e-mail when your data is ready and another one before your data expires to make sure that you are aware of this.

  1. If we only need raw data, can we access it faster?

This is usually the case. During submission of your samples, please be specific that only raw data is needed.

  1. What format is the raw data in?

Your CASAVA demultiplexed raw data is in gzipped FASTQ format. The qualities are encoded in Sanger format (Q33/Illumina 1.9).

  1. Can we get the raw basecall (.bcl) files?

Such requests need to be arranged with the sequencing core itself.

  1. How many mismatches do you allow in index file during demultiplexing? Can this value be changed?

We allow at most 1 mismatch during demultiplexing of the data. This is the default value recommended by Illumina and we have not had any data contamination using this value. If this needs to be tweaked (let’s say you would like 0 mismatches) please make us aware before sequencing has started.