User: ty.thomson

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ty.thomson10
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Posts by ty.thomson

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Comment: C: should I use rsem's summary to genes or tximport's?
... Yup, that transcript is present in tx2gene.  I get tx2gene from the isoforms.results.txt file, so nothing should be missing or differ between RSEM and tximport.  Below are the rows for isoforms.results.txt for that gene in case it helps.  I'll also email you the genes and isoforms rsem files in case ...
written 3.0 years ago by ty.thomson10
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Comment: C: should I use rsem's summary to genes or tximport's?
... Many of these genes end up having a reasonable number of expected counts in other samples, so they don't get filtered out before the edgeR analysis.  In the data set that I'm working with I end up with less than 5% of the differentially expressed genes differing between the two approaches (RSEM and ...
written 3.0 years ago by ty.thomson10
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Comment: C: should I use rsem's summary to genes or tximport's?
... This gene has 12 transcripts, most of which have lengths <700bp.  Two transcripts have lengths in the low thousands of bps, and 1 transcript has length ~25,000bp.  All transcripts have 0 expected counts except for the long transcript which has 1 expected count.   RSEM gives an effective length of ...
written 3.0 years ago by ty.thomson10
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Comment: C: should I use rsem's summary to genes or tximport's?
... Hi Michael, In general the lengths are similar, but some are very different.  In case it helps, I've also included the code that I'm using to generate the results.    > tx2ensembl <- read.delim(rsem.files[1], + stringsAsFactors=F)[,c(1,2)] > > txi_1 <- txi ...
written 3.0 years ago by ty.thomson10
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should I use rsem's summary to genes or tximport's?
... The tximport vignette suggests to just use RSEM’s summary from transcripts to genes (ie, rsem.genes.results.txt) instead of using tximport to do the summary from the transcripts file (i.e., use rsem.isoforms.results.txt, set type="none", and supplying the appropriate column names as arguments).  Pla ...
tximport written 3.0 years ago by ty.thomson10 • updated 3.0 years ago by Michael Love23k

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For should I use rsem's summary to genes or tximport's?

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