Editing BioMicroCenter:News2014 (section)

=== AUGUST 2014 ===
We have set up a collaboration with the University of Massachusetts Medical Center Deep Sequencing Core Facility to provide Pacific Biosciences seqeucning to MIT users. We will be providing initial library preparation and quality control before sending the samples out to Worcester for sequencing. Completed sequence data will be returned through your BioMicro Center public folders. More details about PacBio sequencing can be found on our website.<BR><BR>
The Illumina pipeline has been upgraded to version 1.3. This upgrade includes quality control metrics for RNAseq and paired end reads as well as some changes under the hood to speed up data delivery. These quality control metrics are dependant on genome alignment, so will not be produced for samples aligned to phiX.<BR><BR>
Most of the price increases scheduled for the next fiscal year have been cancelled. We will be re-evaluating the rates in 6 month increments to ensure we remain within our mandated budget constraints.<BR><BR>
Our new co-op students, Austin Hendricks and Adam Perez have joined us and will be working in the Center through December.
The following packages have been added or updated on ROUS in the past few months:	
* trinityrnaseq: r20140413p1
* bedtools: 2.20.1
* bowtie2: 2.2.3
* tophat: 2.0.12
* rsem: 1.2.15
* fastqc: 0.11.2
* bwa: 0.7.10
* pear: 0.9.4
* perl: 5.20.0
* samtools: 1.0
Older versions can still be selected using the module function.  We’ve also created a new mailing list rous_active_users@mit.edu to help keep folks who use Rous regularly up to date. You can sign up for it using Moira.