On Thursday 22 October 2009 12:52:20 Rathi Thiagarajan wrote:
Hello there,
I was really pleased to see that you have the NGS toolbox within Galaxy. I was wondering if there are any plans to include TopHat (http://tophat.cbcb.umd.edu/)and/or Cufflinks (http://cufflinks.cbcb.umd.edu/) into the toolbox as this would be really beneficial.
Also do you have tools to convert fastq format to SAM?
Since SAM is Sequence Alignment/Map Format, the tool you should use is an aligner. I think there are now wrappers for some aligners (bowtie) included in galaxy. The latest releases of bowtie have the option -S to output SAM directly - but I don't know if galaxy enables this option. In the samtools there are many converters for different aligners to SAM. best, ido