Dear Galaxy, Can you tell me which version of Tophat and Cufflinks is being used and whether the Tophat you have uses a GFF or GTF file to help it find splices (this is an option I believe)? Best Wishes, David __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 D.A.Matthews@bristol.ac.uk
Can you tell me which version of Tophat
v1.0.14 In the next couple weeks we'll update to the newest version, v1.1.2
and Cufflinks is being used
The most recent version, v0.9.2
and whether the Tophat you have uses a GFF or GTF file to help it find splices (this is an option I believe)?
Not currently, but we'll add this features in the next couple weeks. Best, J.
I actually have a very basic question on the topic of Cufflinks since I'm a bioinformatics neophyte... I have performed a BWA alignment of Illumina RNA-seq data to the appropriate annotated cDNA database... so it's currently in SAM format. Can I get this data in a form that can be processed by Cufflinks using the tools available on Galaxy or not? So far I haven't been able to figure this out. I assume that Cufflinks is the only (best?) way to look at transcript abundance on Galaxy? Thanks for any help! David Coil, PhD UC Davis Genome Center On Wed, Nov 3, 2010 at 6:17 AM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Can you tell me which version of Tophat
v1.0.14
In the next couple weeks we'll update to the newest version, v1.1.2
and Cufflinks is being used
The most recent version, v0.9.2
and whether the Tophat you have uses a GFF or GTF file to help it find splices (this is an option I believe)?
Not currently, but we'll add this features in the next couple weeks.
Best, J. _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Can I get this data in a form that can be processed by Cufflinks using the tools available on Galaxy or not? So far I haven't been able to figure this out.
You probably know that Cufflinks requires SAM files to be sorted by chromosome name and position. We're working to add the samtools sort to Galaxy. In the meantime, you can sort a SAM file using this workflow: http://main.g2.bx.psu.edu/u/jeremy/w/sort-sam-file-for-cufflinks (Click 'import' to copy it to your workspace.)
I assume that Cufflinks is the only (best?) way to look at transcript abundance on Galaxy?
Currently,Cufflinks is the only way to look at transcript abundance. Best, J.
participants (3)
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David Coil -
David Matthews -
Jeremy Goecks