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Search: Posts Made By: benjamir
Forum: General 10-31-2013, 01:11 PM
Replies: 3
Views: 3,691
Posted By benjamir
Hi Mlacencio, The Illumina TruSeq RNA-seq...

Hi Mlacencio,
The Illumina TruSeq RNA-seq protocol calls for 15 cycle (total RNA 0.1 ug - 4 ug optimized).
A recent single-cell method, Quartz-Seq, performs 21 cycles of whole transcriptome...
Forum: RNA Sequencing 03-13-2013, 05:17 PM
Replies: 10
Views: 3,267
Posted By benjamir
The tuxedo suite is confusing and I feel R is...

The tuxedo suite is confusing and I feel R is more so.

The points on your cummeRbund plots are connected to genes or transcripts in gene_exp.diff or isoform_exp.diff, respectively. I used...
Forum: Bioinformatics 02-12-2013, 01:00 PM
Replies: 6
Views: 1,974
Posted By benjamir
dfhdfh, Tophat 2.0.7 is the first version of...

dfhdfh,
Tophat 2.0.7 is the first version of the program I have ever used. I am also using Bowtie 2.0.6. My initial test run of Tophat has entered its fourth day.

The test is paired-end ( ~100bp...
Forum: Introductions 11-08-2012, 06:39 AM
Replies: 0
Views: 1,278
Posted By benjamir
4th year Illumina User Says Hello Again, I think

I had a previous account through the domain of my previous institution, OSUCCC. I am now at Baylor College of Medicine.

My PhD focused on Cancer Epigenetics in a lab which pioneered DNA...
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