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Forum: RNA Sequencing 02-22-2018, 12:11 PM
Replies: 2
Views: 1,231
Posted By DNAmethylome
Can someone help me on this question? Thank...

Can someone help me on this question?

Thank you very much!
Forum: RNA Sequencing 02-22-2018, 07:52 AM
Replies: 2
Views: 1,231
Posted By DNAmethylome
Can Cufflinks report chimeric transcripts/fusions?

I understand that Cufflinks can report FPKM on novel transcripts (different isoforms) if using proper parameters, but I wonder whether cufflinks is able to report FPKM on chimeric transcripts/gene...
Forum: Bioinformatics 07-27-2016, 05:17 AM
Replies: 2
Views: 1,239
Posted By DNAmethylome
Can anyone help?

Can anyone help?
Forum: Bioinformatics 07-26-2016, 07:58 PM
Replies: 2
Views: 1,239
Posted By DNAmethylome
Tophat chromosome position greater than chromosome size

I use tophat to map the rna-seq reads (paired-end). It seems that some of the reads in the .sam do not make sense. Please see some examples below:

Example line 1:...
Forum: Bioinformatics 08-26-2015, 01:27 PM
Replies: 34
Views: 8,323
Posted By DNAmethylome
Hi, What is your python version?

Hi,

What is your python version?
Forum: Bioinformatics 08-23-2015, 08:19 AM
Replies: 7
Views: 1,245
Posted By DNAmethylome
Hi Zaag, thanks for the input. As you suggested,...

Hi Zaag, thanks for the input. As you suggested, I just re-installed python2.7.10, and ran contra with python 2.7.10, and I still got similar error messages.

Command line:...
Forum: Bioinformatics 08-21-2015, 07:59 AM
Replies: 7
Views: 1,245
Posted By DNAmethylome
Hi, thanks for the input. I am currently...

Hi, thanks for the input.

I am currently using python 2.6.6.
Someone was suggesting these error messages were due to python version issue, and after they switched to python 2.7, the issues were...
Forum: Bioinformatics 08-21-2015, 07:20 AM
Replies: 7
Views: 1,245
Posted By DNAmethylome
Hi,thanks for the reply. I was running this on...

Hi,thanks for the reply.
I was running this on a cluster (using condor). So, this is the path/file that CONTRA would generate during the run. It seems to me that, because of some issues with either...
Forum: Bioinformatics 08-20-2015, 07:05 AM
Replies: 7
Views: 1,245
Posted By DNAmethylome
Can anyone help on this?

Can anyone help on this?
Forum: Bioinformatics 08-14-2015, 01:16 PM
Replies: 34
Views: 8,323
Posted By DNAmethylome
CONTRA error messages

Hi Dr. Li,

I have some problems running CONTRA, I have posted a thread here:
http://seqanswers.com/forums/showthread.php?t=62000

Could you please help me on that?

Thanks a lot!

-J
Forum: Bioinformatics 08-14-2015, 01:11 PM
Replies: 34
Views: 8,323
Posted By DNAmethylome
Hi Dr. Li, I have some problems running...

Hi Dr. Li,

I have some problems running CONTRA, and I have posted a thread here:
http://seqanswers.com/forums/showthread.php?t=62000

Could you please help me on that?

Thanks a lot!

-J
Forum: Bioinformatics 08-14-2015, 12:58 PM
Replies: 7
Views: 1,245
Posted By DNAmethylome
CONTRA error messages (need urgent help!)

Hi,

I am using the tool CONTRA, and getting some error messages as below:
---------
Process Process-1:
Process Process-2:
Traceback (most recent call last):
Traceback (most recent call last):...
Forum: Bioinformatics 10-30-2012, 12:44 PM
Replies: 0
Views: 789
Posted By DNAmethylome
New to NGS field.. Need advices~!!

Hi folks,

I am new to SEQanswer. A brief introduction about myself: I have been a computational person (PhD student studying Genetic Epidemiology). I have used SAS and R to handle the GWAS data a...
Showing results 1 to 13 of 13

 


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