Trouble with importing transcript counts with Salmon
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Jenni • 0
@6c7ebb74
Last seen 7 days ago
United States

I am working on importing my quant.sf files from salmon into R studio for analysis with edgeR. I'm having an issue matching my transcript IDs from salmon to the dataframe I made matching transcript ID to gene ID. The salmon files have a decimal "ENSXETT00000115366.1" but the dataframe I made from the ensemble genome does not "ENSXETT00000066481". Could this be the problem? If so how do I remove the decimals without messing up my data? If it's not the issue, is there something else I could be doing wrong?

Code should be placed in three backticks as shown below

xen_txi <- tximport(xen_files, type = "salmon", tx2gene = xen_tx2gene, ignoreAfterBar=TRUE)

This returns the following error:

"Error in .local(object, ...) : None of the transcripts in the quantification files are present in the first column of tx2gene. Check to see that you are using the same annotation for both.

Example IDs (file): [ENSXETT00000115366.1, ENSXETT00000107576.1, ENSXETT00000106130.1, ...]

Example IDs (tx2gene): [ENSXETT00000066481, ENSXETT00000108741, ENSXETT00000108618, ...]

This can sometimes (not always) be fixed using 'ignoreTxVersion' or 'ignoreAfterBar'."

# please also include the results of running the following in an R session

sessionInfo( )

R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Monterey 12.5

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 

Salmon tximport RNAseq EdgeR • 56 views
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Entering edit mode
ATpoint ★ 1.9k
@atpoint-13662
Last seen 16 minutes ago
Germany

Use ignoreTxVersion=TRUE, these numbers like .1 are version numbers, and the option will remove that so it matches with tx2gene, it's basically a gsub("\\..", "", x). ignoreAfterBar is for bars (|) as often seen in GENCODE files.