Can I apply tximport to transcript-level estimates obtained using cufflinks (cuffquant and cuffnorm) ??
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@leiamax2020-24199
Last seen 7 months ago

Hi, I am new to Tximport. In the vignette i see that cufflinks is listed among the tools used for transcript abundance,

(library(tximportData)
dir <- system.file("extdata", package = "tximportData")
list.files(dir) )

However I cant find any command or example that show how to import cufflinks files ("isoforms.counttable" "isoforms.fpkmtable" "significant_isoforms.txt")

Can you please provide some help?

Thank you in advance

tximport Cufflink Tutorial • 96 views
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You may want to edit your posts and add code formatting (backticks, select the text to format and click the 101010 button) to the cufflinks file names to bypass _ being parsed as a markdown character.

code_formatting

Your text without code formatting: "isoforms.counttable", "isoforms.fpkmtable", "significant_isoforms.txt" (see how the first two underscore characters italicize words between them)

Your text with code formatting: isoforms.count_table, isoforms.fpkm_table, significant_isoforms.txt

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