Couldn't find matching transcriptome
1
0
Entering edit mode
Fei Liu • 0
@fei-liu-22054
Last seen 14 months ago

Hi all, when I use tximeta, follow the usage http://www.bioconductor.org/packages/release/bioc/vignettes/tximeta/inst/doc/tximeta ,

salmon index -t Homo_sapiens.GRCh38.cdna.all.fa.gz Homo_sapiens.GRCh38.ncrna.fa.gz -i GRCh38.index

and then

files <- file.path(dir,"quant.sf")
file.exists(files)
coldata <- data.frame(files, names="control_1", condition="A", stringsAsFactors=FALSE)

fastaFTP <- c('~/downloads/REFERENCE/Homo_sapiens.GRCh38.cdna.all.fa.gz','~/downloads/REFERENCE/Homo_sapiens.GRCh38.ncrna.fa.gz')

gtfPath <- '~/downloads/REFERENCE/Homo_sapiens.GRCh38.98.gtf.gz'

makeLinkedTxome <- function(indexDir,source,organism,release,genome,fasta,gtf,write=TRUE,jsonFile)
{indexJson <- file.path(indexDir,"info.json")
indexList <- fromJSON(indexJson)
indexSeqHash <- indexList$value0$SeqHash
index <- basename(indexDir)
std.sources <- c("Gencode", "Ensembl")
for (src in std.sources) {
   if (tolower(source) == tolower(src)) {
        source <- src
      }
}
}

makeLinkedTxome(indexDir=indexDir,source="Ensembl",organism="Homo sapiens", release="98", genome="GRCh38", fasta=fastaFTP, gtf=gtfPath, write=FALSE)

se <- tximeta(coldata)

error:

importing quantifications
reading in files with read_tsv
1 
couldn't find matching transcriptome, returning un-ranged SummarizedExperiment

I want to ask why this error occurs? Thank you all

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6
 [2] GenomicFeatures_1.36.4
 [3] AnnotationDbi_1.46.1
 [4] Biobase_2.44.0
 [5] GenomicRanges_1.36.1
 [6] GenomeInfoDb_1.20.0
 [7] IRanges_2.18.3
 [8] S4Vectors_0.22.1
 [9] BiocGenerics_0.30.0
[10] tximeta_1.2.2
[11] RJSONIO_1.3-1.4

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3                  lattice_0.20-38
 [3] prettyunits_1.1.0           Rsamtools_2.0.2
 [5] Biostrings_2.52.0           assertthat_0.2.1
 [7] zeallot_0.1.0               digest_0.6.22
 [9] BiocFileCache_1.8.0         R6_2.4.1
[11] backports_1.1.5             RSQLite_2.2.0
[13] httr_1.4.1                  pillar_1.4.3
[15] zlibbioc_1.30.0             rlang_0.4.2
[17] progress_1.2.2              lazyeval_0.2.2
[19] curl_4.3                    blob_1.2.0
[21] Matrix_1.2-17               BiocParallel_1.18.1
[23] readr_1.3.1                 stringr_1.4.0
[25] ProtGenerics_1.16.0         RCurl_1.95-4.13
[27] bit_1.1-15.1                biomaRt_2.40.5
[29] DelayedArray_0.10.0         compiler_3.6.1
[31] rtracklayer_1.44.4          pkgconfig_2.0.3
[33] tximport_1.12.3             tidyselect_0.2.5
[35] SummarizedExperiment_1.14.1 tibble_2.1.3
[37] GenomeInfoDbData_1.2.1      matrixStats_0.55.0
[39] XML_3.98-1.20               crayon_1.3.4
[41] dplyr_0.8.3                 dbplyr_1.4.2
[43] GenomicAlignments_1.20.1    bitops_1.0-6
[45] rappdirs_0.3.1              grid_3.6.1
[47] jsonlite_1.6                DBI_1.1.0
[49] AnnotationFilter_1.8.0      magrittr_1.5
[51] stringi_1.4.5               XVector_0.24.0
[53] vctrs_0.2.1                 ensembldb_2.8.1
[55] tools_3.6.1                 bit64_0.9-7
[57] glue_1.3.1                  purrr_0.3.3
[59] hms_0.5.3                   memoise_1.1.0
tximeta • 104 views
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0
Entering edit mode
@mikelove
Last seen 18 hours ago
United States

Firstly, if you are using Ensembl human transcripts, everything should work out of the box, even combining cDNA and ncRNA.

Could you update to the latest version of tximeta (either in release or devel) which includes Ensembl 99 already?

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0
Entering edit mode

Thank you very much. The problem has been solved. Best regards!

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