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
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
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
3 matches
Mail list logo