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Forum: RNA Sequencing 10-31-2012, 06:53 PM
Replies: 0
Views: 870
Posted By taozuo
tophat-uniquely mapped reads-with or without -g 1 option

Hi:

I recently compared the uniquely mapped reads generated with and without -g 1 option. However, I got very different answers.

with -g 1 option, the mapped reads were 9,737,100, about 68% of...
Forum: RNA Sequencing 06-29-2012, 06:50 AM
Replies: 0
Views: 1,860
Posted By taozuo
Uniquely mapped reads or multiple mapped reads?

Hi Fellows:
For calling differentially expressed genes from RNA-seq data, do you use uniquely mapped reads or multiply mapped reads as well? which one is better for this purpose? Thanks
Forum: RNA Sequencing 03-02-2012, 03:17 PM
Replies: 1
Views: 1,708
Posted By taozuo
Cufflinks followed by Microarray-like statistical test ??

For cufflinks, I know that cuffdiff can perform statistical test for identifying differential expressed genes. And I also know that there are several other tools could conduct statistical analysis...
Forum: RNA Sequencing 10-17-2011, 08:28 PM
Replies: 4
Views: 4,401
Posted By taozuo
I am not quite sure right now for your case. But...

I am not quite sure right now for your case. But I did this before and I can get all the comparisons. For example, if I open the gene_exp.diff file, I will have the q1 vs q2 first. And when I...
Forum: RNA Sequencing 10-17-2011, 02:34 PM
Replies: 4
Views: 4,401
Posted By taozuo
For Question 1: Yes, Cuffdiff would only...

For Question 1:

Yes, Cuffdiff would only generate one output even though you have more than one comparisons. However, all other comparisons are also included in that file. Check the output file...
Forum: RNA Sequencing 10-14-2011, 03:05 PM
Replies: 5
Views: 6,819
Posted By taozuo
Hi Ash: I am meeting the same problem as you...

Hi Ash:

I am meeting the same problem as you did and I have not found any solutions yet.

Could you post some graphs to explain how you did fix it? I wanna know what your original chromosome...
Forum: RNA Sequencing 10-12-2011, 06:16 AM
Replies: 6
Views: 2,470
Posted By taozuo
Hi Artur: I do not know the exact solution...

Hi Artur:

I do not know the exact solution to solve the problem, but when I tried like this, It does work right now.

1. sudo cp .../bowtie bowtie-build bowtie-inspect /usr/bin
2. sudo cp...
Forum: RNA Sequencing 10-06-2011, 07:24 AM
Replies: 6
Views: 2,470
Posted By taozuo
Tophat error 2

Hi Folks:

I met a problem while aligning RNA-seq data with tophat.

It shows like this:

[Wed Oct 5 17:10:55 2011] Beginning TopHat run (v1.3.2)...
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