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Question: Embl 66 Genome For Rnaseq Analysis
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gravatar for Karthik Srinivasan
6.7 years ago by
Karthik Srinivasan • 10
Karthik Srinivasan • 10 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:HYPERLINK "tel:+912242554282"+912242554282 | M:HYPERLINK "tel:+919987014704"+919987014704 Oracle Health Sciences Global Business Unit 6'th Floor, Silver Metropolis, W.E.Highway, Goregaon(E) | 400063 Mumbai
rna-seq tophat • 899 views
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modified 6.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.7 years ago by Karthik Srinivasan • 10
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gravatar for Jennifer Hillman Jackson
6.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
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
ADD COMMENT • link written 6.7 years ago by Jennifer Hillman Jackson ♦ 25k
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