Dear all

I have in my project single end reads (50 bp) for some samples and paired end 
reads (100 bp frw and rev) for  the other samples. I had to re-sequence some of 
the samples of which I have paired-end reads. However the re-sequence data I 
receives is single-end reads of 250 bp. Tophat wont allow mapping single and 
paired-end reads together. It says the result will look bad. They do mention 
that you can convert the junctions.bed file (output of Tophat) with 
bed_to_juncs using the -j option. I quote for TopHat manual "run TopHat on the 
2nd set of reads using the -j option to supply the junctions file produced by 
be_to_juncs in the previous step". This is supposed to work but I didn't get it 
to work. Any suggestion on how I should go about analyzing this data? 

Kind regards

Lizex

>>> Nate Coraor  02/15/13 5:48 PM >>>
On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote:

> To whom it may concern:
>  
> The History panel on the right side of the Galaxy page is taking a very very 
> long time to load. Also, when it does load, I have tired to save my bam files 
> and the transmissions gets truncated to ~7000kb - 8000kb of data. All of my 
> .bam files are several GB.
>  
> Some times, when I retry tor download the data, it succeeds and other times 
> it is again truncated. The size of the truncation may be different for the 
> same file on the retry attempt.
>  
> Is there a problem with Galaxy?

Hi Mike,

There are some performance problems with the Main site that we are currently 
investigating.  Thanks for the information and we apologize for the problems.

--nate

>  
> Thanks,
> Mike
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