Re: [galaxy-user] cufflinks analysis using .bam files generated by LifeScope (ABI 5500 Sequencer)

Hello Davide, If the data does represent alignments (not just sequence), then there is one more item to check for. Another team member reminded me that Cufflinks requires an XS custom tag in an input SAM file (or any compressed BAM file that represents it). Details are here from the

[galaxy-user] How to Provide .gtf file to tophat2

I'm trying to translate this command line run into the Galaxy GUI but I'm not seeing a place to specify the .gtf file. Does anyone know? tophat2 -p 8 -G /groups/bowtie2_index/mRNA.gtf -o /groups/hp_1 /groups/genome /groups/reads.fastq thanks, Greg

Re: [galaxy-user] How to Provide .gtf file to tophat2

That's very helpful! Thanks. -Greg On Tue, Dec 18, 2012 at 11:39 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Greg, Open up TopHat settings to use: to Full Parameter list to find the option: Use Own Junctions: and set this to Yes. There will be a new option underneath it for Use Gene