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Forum: RNA Sequencing 02-21-2015, 09:05 AM
Replies: 0
Views: 1,870
Posted By Kolamite
Tophat error with Cuffmerged GTF

I'm trying to run Tophat 2.0.13 (bowtie 1.1.1) on colorspace csfasta and qual files using a GTF produced by Cuffmerge (Cufflinks 2.2.1) as a -G option. Cuffmerge was run on 8 Cufflinked...
Forum: RNA Sequencing 10-20-2014, 02:56 PM
Replies: 0
Views: 948
Posted By Kolamite
Tophat-fusion clarification: orientation

This seems like an obvious question, but I couldn't find an obvious answer anywhere.

Tophat-fusion-post output includes the orientation of each fusion partner. I'm noticing that a really high...
Forum: Bioinformatics 07-30-2014, 02:22 PM
Replies: 5
Views: 3,028
Posted By Kolamite
Combining RNA-seq datasets

I searched a lot of threads here and elsewhere without finding anything exactly like this.

I have two RNA-seq datasets from different dates and different platforms. Split between them are 4...
Forum: Bioinformatics 07-01-2014, 09:30 AM
Replies: 0
Views: 881
Posted By Kolamite
Tophat-fusion interpretation questions

I'm new to RNA-sequencing in general and Tophat in particular, and I've got a few embarrassingly basic questions about the output that I was hoping someone could me help with.

In the results file,...
Forum: Sample Prep / Library Generation 01-22-2013, 10:26 AM
Replies: 1
Views: 1,253
Posted By Kolamite
Bioruptor - Poor Fragmentation Results

Hey,

I'm trying to perform a ChIP-seq experiment for a transcription factor using the Diagenode bioruptor.

I'm getting very poor fragmentation at 30 minutes (3x10 cycles, high power, 30s on,...
Forum: Bioinformatics 11-15-2012, 08:49 AM
Replies: 2
Views: 2,902
Posted By Kolamite
Gotcha, I was misinformed. Thanks!

Gotcha, I was misinformed.

Thanks!
Forum: Bioinformatics 11-13-2012, 01:09 PM
Replies: 2
Views: 2,902
Posted By Kolamite
Tophat Cygwin Build from source error: aio.h

I'm running Cygwin on a Windows 7 machine and trying to build Tophat from source following this tutorial:
http://tophat.cbcb.umd.edu/tutorial.html

I installed everything available through the...
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