Tophat Etc

Question: Tophat Etc

8.1 years ago by

United Kingdom

David Matthews • 630 wrote:

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

gff cufflinks rna-seq • 834 views

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modified 8.1 years ago by Jeremy Goecks • 2.2k • written 8.1 years ago by David Matthews • 630

8.1 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

[cc'ing galaxy-user for informational and archival purposes] The problems you're seeing with Cufflinks may be due to your use of BWA and, consequently, a lack of splice junctions. Is there any particular reason that you're using BWA to map your RNA- seq data? BWA isn't appropriate for mapping RNA-seq data unless you make modifications to handle splice junction mapping; it would be difficult to make these modifications in Galaxy. There are mappers designed specifically for RNA-seq data; in Galaxy, you should generally use Tophat to map your RNA-seq data. I encourage you to try mapping your data with Tophat and seeing if that solves your problems. Thanks, J.

ADD COMMENT • link written 8.1 years ago by Jeremy Goecks • 2.2k

8.1 years ago by

Jeremy Goecks • 2.2k

Jeremy Goecks • 2.2k wrote:

v1.0.14 In the next couple weeks we'll update to the newest version, v1.1.2 The most recent version, v0.9.2 Not currently, but we'll add this features in the next couple weeks. Best, J.

ADD COMMENT • link written 8.1 years ago by Jeremy Goecks • 2.2k

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

ADD REPLY • link written 8.1 years ago by David Coil • 20

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.) Currently,Cufflinks is the only way to look at transcript abundance. Best, J.

ADD REPLY • link written 8.1 years ago by Jeremy Goecks • 2.2k

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