What Is The Effect Of Using Ordering In The Exonby Function In R (Bioconductor)

Question

[Jetse]

Hello everyone,

I am using the programming language R, with this language I first want to download exons from the UCSC website. Now I'm using this R code:

txdb <- makeTranscriptDbFromUCSC( genome='hg19', tablename='refGene' )
tx_by_exon <- exonsBy(txdb, 'tx')

When I'm changing the 'tx' to 'gene', the data is totally differend. When converting to a data.frame (with as.data.frame), the by gene ordered list is only half of the unordered list... In the manual this is described as: One of ‘"gene"’, ‘"exon"’, ‘"cds"’ or ‘"tx"’. Determines the grouping. And I thought grouping doesn't change the data...

I use this data to check which mapping tool to use, tophat or bwa. The difference between the ordering, makes or tophat much better (when not ordering), or bwa just a little bit better (when ordering by gene)... The largest difference between those mapping tools is the RNA splicing. So this change in ordering has something to do with the RNA splicing...

Anyone knows what this difference is?

Answer 1

[Jeremy Leipzig]

grouping changes the data

you can expect a lot more exons by transcript because multiple transcripts exist for the same gene, so you will see that same exon appear multiple times under different transcript names