[galaxy-user] subtract

Hello, I am using the subtract (whole dataset) tool. I converted my fastq file to tabular with 2 columns: 1. Identifier and 2. sequence. I then selected (a few) lines that match an expression from this initial tabular file and am trying to get a final dataset that is devoid of reads with the

[galaxy-user] Displaying bed files in ucsc

Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments are(based on the start and end coordinates) with numerical scores beside each fragment. How do I view the file as a histogram format? What format will I need

Re: [galaxy-user] Displaying bed files in ucsc

will be enough, if not you might be required to enter a track line. See UCSC for details. On Thu, May 10, 2012 at 9:04 PM, Xianrong Wong won...@gmail.com wrote: Hello, I have a bed file in this format: chr# start end scores. I tried to view it in ucsc main but it showed only where the fragments

[galaxy-user] replace function on galaxy

Hello, I have been using the compute function in galaxy to replace sequences with delimiters for processing my reads. I realized that the replace code in compute no longer works. Is there any other way to replace sequences with delimiters? Jose

Re: [galaxy-user] Read simulator

Hi, I've been trying to use the extra DNA tool but I keep getting an error: Traceback (most recent call last): File /galaxy/main/server/tools/extract/extract_genomic_dna.py, line 300, in if __name__ == __main__: __main__() File /galaxy/main/server/tools/extract/extract_genomic_dna.py, line 113,