tximport for salmon output

[alyamahmoud]

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

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:

txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, reader = read_tsv)

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

[sulicon]

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

[granger]

Thanks sulicon, that helped.
btw a quick way to remove those rows in R:

tx2gene <- tx2gene[!duplicated(tx2gene$ens_id_version), ]

[peromhc]

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.

Thanks sulicon, that helped.
btw a quick way to remove those rows in R:

tx2gene <- tx2gene[!duplicated(tx2gene$ens_id_version), ]

[granger]

@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.