Error: couldn't find matching transcriptome when using Salmon Mouse index from Ensembl

[diegoalzatec86]

Hello I'm trying to run tximeta on quant.sf files obtained with Salmon. I create an index for the Mouse Transcriptome obtained from Ensembl. $ curl ftp://ftp.ensembl.org/pub/release-100/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz -o mmus.fa.gz

After creating my coldata file specifying files and names I run > se<-tximeta(coldata)

importing quantifications reading in files with read_tsv 1 2 3 4 5 6 7 8 9 10 11 12

tximeta needs a BiocFileCache directory to access and save TxDb objects. Do you wish to use the default directory: '/Users/user/Library/Caches/BiocFileCache'? If not, a temporary directory that is specific to this R session will be used.

You can always change this directory later by running: setTximetaBFC() Or enter [0] to exit and set this directory manually now.

1: Yes (use default) 2: No (use temp)

Selection: 1 /Users/user/Library/Caches/BiocFileCache does not exist, create directory? (yes/no): Yes couldn't find matching transcriptome, returning un-ranged SummarizedExperiment

what can be causing that tximeta does not recognize the mouse transcriptome from Ensembl?

[mikelove]

My first guess would be you are using an older version of tximeta. The latest release matches with the latest Ensembl release, but older versions of tximeta cannot be updated.

[diegoalzatec86]

Thanks for answering. I'm totally new in this so I just installed tximeta for the first time yesterday (May 20-2020). However I went ahead and reinstall tximeta today, but the problem persist. Is there any other option?

[mikelove]

You can use sessionInfo to find out your software versions. Bioconductor packages (if installed via BiocManager) are linked to R version. So if you are using old version of R => old version of Bioc => you will get old version of tximeta, which can't be updated. So when Ensembl does a new release, the old version of tximeta won't recognize it. But first, use sessionInfo() and report here your version.

[diegoalzatec86]

Thanks, Here is the report.

sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.15.4

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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

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

other attached packages: [1] tximeta_1.0.3

loaded via a namespace (and not attached): [1] Rcpp_1.0.4.6 lattice_0.20-41 prettyunits_1.1.1
[4] Rsamtools_1.34.1 Biostrings_2.50.2 assertthat_0.2.1
[7] digest_0.6.25 BiocFileCache_1.6.0 R6_2.4.1
[10] GenomeInfoDb_1.18.2 stats4_3.5.1 RSQLite_2.2.0
[13] httr_1.4.1 pillar_1.4.4 zlibbioc_1.28.0
[16] rlang_0.4.6 GenomicFeatures_1.34.8 progress_1.2.2
[19] lazyeval_0.2.2 curl_4.3 rstudioapi_0.11
[22] blob_1.2.1 S4Vectors_0.20.1 Matrix_1.2-18
[25] BiocParallel_1.16.6 readr_1.3.1 stringr_1.4.0
[28] ProtGenerics_1.14.0 RCurl_1.98-1.2 bit_1.1-15.2
[31] biomaRt_2.38.0 DelayedArray_0.8.0 compiler_3.5.1
[34] rtracklayer_1.42.2 pkgconfig_2.0.3 BiocGenerics_0.28.0
[37] tximport_1.10.1 tidyselect_1.1.0 SummarizedExperiment_1.12.0 [40] tibble_3.0.1 GenomeInfoDbData_1.2.0 IRanges_2.16.0
[43] matrixStats_0.56.0 XML_3.99-0.3 crayon_1.3.4
[46] dplyr_0.8.5 dbplyr_1.4.3 GenomicAlignments_1.18.1
[49] bitops_1.0-6 rappdirs_0.3.1 grid_3.5.1
[52] jsonlite_1.6.1 lifecycle_0.2.0 DBI_1.1.0
[55] AnnotationFilter_1.6.0 magrittr_1.5 stringi_1.4.6
[58] XVector_0.22.0 ellipsis_0.3.1 vctrs_0.3.0
[61] ensembldb_2.6.8 tools_3.5.1 bit64_0.9-7
[64] Biobase_2.42.0 glue_1.4.1 purrr_0.3.4
[67] hms_0.5.3 parallel_3.5.1 yaml_2.2.1
[70] AnnotationDbi_1.44.0 BiocManager_1.30.10 GenomicRanges_1.34.0
[73] memoise_1.1.0

[mikelove]

Your version of R is from July 2018, and this is paired with Bioconductor 3.8.

This was the version of tximeta back then:

http://bioconductor.org/packages/3.8/bioc/html/tximeta.html

You can see the current version by changing 3.8 in the URL to "release" (this link always points to the latest release, which may not be the same as what you have on your system, as in your case):

http://bioconductor.org/packages/release/bioc/html/tximeta.html

This is the same (as of May 2020) as the URL:

http://bioconductor.org/packages/3.11/bioc/html/tximeta.html

There have been two years of updates to Bioconductor packages, including both bug fixes and additional features, so if you are just starting out, it's a good idea to use the latest versions. Here are some instructions on installing the latest version of R/Bioconductor:

http://bioconductor.org/install/

I'm going to close this issue, as I think we've diagnosed what happened, and if you have further questions about tximeta, feel free to post them here:

https://suppport.bioconductor.org

and tag the post with "tximeta", so I will get an automatic email from the system to reply there.

[diegoalzatec86]

Perfect. Thank you!!