Question: How to get gene sequences (DEGs) not transcripts sequences?
gravatar for ahran737
20 months ago by
ahran7370 wrote:

Hello, my name is one of Galaxy user in Korea. I conducted cuffmerge -> cuffquant -> cuffnorm -> cuffdiff, and got transcripts and genes FPKM counts and data including sequences locus from genome that I put into history. Following all these procedures, I already got transcript sequences as galaxy team informed. I made an effort to get gene sequences many times (I am struggling though...).

For instance, my RNA-seq data reveals about 45,000 transcripts and 20000 genes. Among these genes, there are different sequences despite of same gene as like below... XLOC_000012 XLOC_000012 - AGQT01000036.1:18234-28315 AGQT01000036.1:18235-28315 TSS19,TSS20,TSS21
XLOC_000013 XLOC_000013 - AGQT01000036.1:18234-28315 AGQT01000036.1:18235-28315 TSS22
XLOC_000014 XLOC_000014 - AGQT01000036.1:18234-28315 AGQT01000036.1:18235-28315 TSS23

I want to annotate and analyze with gene levels, not transcript. How to get gene sequences in galaxy?

rna-seq galaxy • 345 views
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