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Forum: RNA Sequencing 05-08-2012, 12:20 AM
Replies: 5
Views: 3,876
Posted By ae_ucla
I redownloaded tophat2.0.0 today and reran it...

I redownloaded tophat2.0.0 today and reran it with no errors. Previously the tophat_reports program at the end (generating final output) would give me the above error. An update fixed it, and it...
Forum: RNA Sequencing 05-04-2012, 05:51 PM
Replies: 5
Views: 3,876
Posted By ae_ucla
It looks like my problem is that I need a higher...

It looks like my problem is that I need a higher version of Boost C++ libraries.
Forum: RNA Sequencing 05-04-2012, 04:18 PM
Replies: 5
Views: 3,876
Posted By ae_ucla
Error with Tophat2 no output

I just ran tophat2 on some data that I previously have alligned. It goes until the last step and I get an error and no output:

[2012-05-03 19:05:31] Beginning TopHat run (v2.0.0)...
Forum: RNA Sequencing 06-16-2011, 02:37 PM
Replies: 5
Views: 5,201
Posted By ae_ucla
Has anyone used Cufflinks for microRNA data?

Has anyone used Cufflinks for microRNA data?
Forum: RNA Sequencing 04-01-2011, 12:03 PM
Replies: 1
Views: 5,172
Posted By ae_ucla
unaligned reads of tophat

Does anyone know a way to see which reads from tophat are unaligned? I figured out how to do this in bowtie with the --un and --max options, but does someone have a way to do this in tophat?
Forum: RNA Sequencing 03-22-2011, 02:37 PM
Replies: 3
Views: 2,854
Posted By ae_ucla
Thank you very much for your response. I have...

Thank you very much for your response. I have actually changed my -c option to 0, seeing that there are genes with a smaller amount of reads that still can be differentially expressed. Can anyone...
Forum: RNA Sequencing 03-07-2011, 09:13 PM
Replies: 3
Views: 2,854
Posted By ae_ucla
acceptable -c threshold for cuffdiff?

Hi, I am using cuffdiff on single end illumina data. I naturally get a lot more significantly differentially expressed genes if I lower my threshold from 500 to 300, for example. When I use the...
Forum: RNA Sequencing 10-22-2010, 03:54 PM
Replies: 1
Views: 2,591
Posted By ae_ucla
Hi, I just wanted to update my previous post. I...

Hi, I just wanted to update my previous post. I previously ran cufflinks in the following way, in order to find known and novel transcripts:
I ran tophat without a reference, ran cufflinks without a...
Forum: RNA Sequencing 10-20-2010, 05:15 PM
Replies: 1
Views: 2,591
Posted By ae_ucla
Multiple gene entries in cuffdiff output

Hi, I am using the newest version of cufflinks. My gene_exp.diff output has multiple entries for the same gene.
Any advice on how to interpret this?
thanks, my output is below:...
Forum: Bioinformatics 10-03-2010, 03:33 PM
Replies: 18
Views: 4,961
Posted By ae_ucla
Yes, I have the same problem, I posted this in...

Yes, I have the same problem, I posted this in another thread:
http://seqanswers.com/forums/showthread.php?t=7109
Forum: RNA Sequencing 10-01-2010, 04:18 PM
Replies: 5
Views: 3,172
Posted By ae_ucla
Error with cuffdiff, version 0.9.0

Hi, I am running the newest version of cufflinks with cuffdiff and am getting the error:
"Error: this SAM file doesn't appear to be correctly sorted!
current hit is at chr3:3018707, last one was...
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