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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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