Tophat To Ngs Toolbox

Question: Tophat To Ngs Toolbox

9.1 years ago by

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? Thanking you in advance. Cheers, Rathi -- Rathi Thiagarajan Institute for Molecular Bioscience University of Queensland, St. Lucia, QLD 4072 AUSTRALIA

rna-seq cufflinks • 717 views

ADD COMMENT • link •

modified 9.1 years ago by Matthias Dodt • 110 • written 9.1 years ago by Rathi Thiagarajan • 50

9.1 years ago by

Ido M. Tamir • 280

Austria

Ido M. Tamir • 280 wrote:

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

ADD COMMENT • link written 9.1 years ago by Ido M. Tamir • 280

9.1 years ago by

Matthias Dodt • 110

Matthias Dodt • 110 wrote:

Hi Rathi! I wrote a tophat wrapper myself- you can use it if u want, the files are attached. you need to adapt the BOWTIE_INDEXES path in the toohatwrapper.py and the bowtie path. if these variables are already set then you can just remove the lines between "#path settings" and "#path settings end". And you must include the tophat.xml in the tool-conf.xml in the main galaxy folder - in a section of your choice. Let me know if u find any errors- greetings mat Rathi Thiagarajan schrieb:

ADD COMMENT • link written 9.1 years ago by Matthias Dodt • 110

Please log in to add an answer.

Similar posts • Search »