Hello Karthik,
Because it is sourced from UCSC, the GRCh37 genome is available in Galaxy as "hg19". The full name is: Human Feb. 2009 (GRCh37/hg19) (hg19)
This aligns with how Ensembl also understands the content: http://lists.ensembl.org/pipermail/dev/2012-February/002180.html
For RNA-seq analysis (and sometime other types of analysis) you may need to adjust other input data's chromosome naming to match the UCSC format. This is explained in the RNA-seq FAQ: https://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq5
The data in the FTP link you provide is annotation data. To use annotation data with the RNA-seq pipeline, a GTF file would be a good format. The RNA-seq tool pages have a link out to Ensembl, but any source from the same genome is OK (UCSC, etc.).
Best,
Jen Galaxy team
On 4/2/12 4:14 AM, Karthik Srinivasan wrote:
Hi,
How do I run Tophat and RNA-Seq analysis using the GRCH37- embl 66 genome? I noticed there is no input for this genome version.
Can I construct a reference genome from the following embl format source sequences: ftp://ftp.ensembl.org/pub/release-66/embl/homo_sapiens/, and map it against my RNAseq data?
Regards,
Karthik
Karthik Srinivasan | Senior Application Engineer P:+912242554282 tel:+912242554282 | M:+919987014704 tel:+919987014704 OracleHealth Sciences Global Business Unit 6'th Floor, Silver Metropolis, W.E.Highway, Goregaon(E) | 400063 Mumbai
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