Question: transcript to gene mapping after sleuth run
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gravatar for bioinfo8
3.1 years ago by
bioinfo8120
bioinfo8120 wrote:

Hi,

I have ran kallisto and sleuth for my RNA-seq data and used the following for transcript to gene mapping before running sleuth:

mart_11 <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "organism_gene_ensembl", host = 'mar2015.archive.ensembl.org')

t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"), mart = mart_11)

t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name)

Now I have sleuth output and realized that some of the transcripts has NA in ens_gene and ext_gene. I found out that in the recent assembly there is information regarding this. Would anyone can guide me an easy way to update this information in my sleuth output and also adding gene names instead of transcript IDs. Otherwise, I have to run sleuth again by creating new t2g.

Thanks!

kallisto rna-seq biomart sleuth R • 1.1k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by bioinfo8120
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