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Old 08-24-2016, 12:20 AM   #1
alyamahmoud
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Location: Egypt, Saudi Arabia

Join Date: Nov 2013
Posts: 29
Default tximport for salmon output

I am trying to use tximport to analyze salmon output, but I am stuck with the error below and not sure which files are the problematic ones

Code:
summarizing abundance
summarizing counts
summarizing length
Error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
In addition: Warning message:
In names(aveLengthSampGene) == rownames(lengthMat) :
  longer object length is not a multiple of shorter object length
this is how I run tximport:
Code:
txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, reader = read_tsv)

Code:
sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

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

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] readr_1.0.0        tximport_1.0.3     tximportData_1.0.2

loaded via a namespace (and not attached):
[1] assertthat_0.1 tools_3.3.1    tibble_1.1     Rcpp_0.12.6    tcltk_3.3.1
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Old 08-24-2016, 12:01 PM   #2
sulicon
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Location: Los Angeles

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Default

I happened to meet exactly the same error this morning. It turns out there is something "wrong" in the transcript to gene mapping (tx2gene). I am using GENCODE mouse v10 transcriptome and the tx2gene mapping file provided by GENCODE have lines like this:

ENSMUST00000023648.5 4930553J12Rik
ENSMUST00000023648.5 Krtap15
ENSMUST00000187823.1 4930553J12Rik
ENSMUST00000187823.1 Krtap15

The same transcript is mapped to two gene symbols. I solved this issue by simply removing the lines with "4930553J12Rik". Hope this helps
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Old 12-01-2016, 10:21 AM   #3
granger
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Location: United Kingdom

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Smile

Thanks sulicon, that helped.
btw a quick way to remove those rows in R:
Code:
tx2gene <- tx2gene[!duplicated(tx2gene$ens_id_version), ]
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Old 07-11-2017, 10:04 AM   #4
peromhc
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Location: Durham, NH

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Isn't aggregating the counts from multiple transcripts to a single gene kinda the point of tximport? Seems like removing the duplicate gene id's is removing important information.


Quote:
Originally Posted by granger View Post
Thanks sulicon, that helped.
btw a quick way to remove those rows in R:
Code:
tx2gene <- tx2gene[!duplicated(tx2gene$ens_id_version), ]
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Old 07-12-2017, 01:59 AM   #5
granger
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@peromhc Yes it is, but the problem with the above tx2gene mapping is that it maps one transcript to multiple genes. Best is to keep track of gene ids removed.

A similar problem I came across: multiple ENS gene ids which encode the same gene product (e.g. have the same HUGO name). Thousands of HUGO genes have multiple ENS ids and that can be a problem.
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rnaseq analysis, salmon, tximport

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