Error in makeTxDbFromGFF(txomeInfo$gtf)
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Entering edit mode
Jag • 0
@7ef3b2eb
Last seen 21 days ago
United States

Hello, I am trying to perform DESeq2 on Salmon indexed mouse data. I am running into the following error when trying to execute tximeta.

importing quantifications
> se <- tximeta(coldata)
reading in files with read_tsv
1 2 3 4 
found matching linked transcriptome:
[ GENCODE - Mus musculus - release M27 ]
useHub=TRUE: checking for TxDb via 'AnnotationHub'
snapshotDate(): 2021-05-18
did not find matching TxDb via 'AnnotationHub'
building TxDb with 'GenomicFeatures' package
Error in makeTxDbFromGFF(txomeInfo$gtf) : 
  Cannot detect whether 'file' is a GFF3 or GTF file. Please use the 'format' argument to specify the format ("gff3" or
  "gtf").

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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_1.10.0

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.24.0           bitops_1.0-7                  matrixStats_0.60.1            bit64_4.0.5                  
 [5] filelock_1.0.2                progress_1.2.2                httr_1.4.2                    GenomeInfoDb_1.28.4          
 [9] tools_4.1.0                   utf8_1.2.2                    R6_2.5.1                      DBI_1.1.1                    
[13] BiocGenerics_0.38.0           lazyeval_0.2.2                withr_2.4.2                   tidyselect_1.1.1             
[17] prettyunits_1.1.1             bit_4.0.4                     curl_4.3.2                    compiler_4.1.0               
[21] Biobase_2.52.0                xml2_1.3.2                    DelayedArray_0.18.0           rtracklayer_1.52.1           
[25] readr_2.0.1                   rappdirs_0.3.3                stringr_1.4.0                 digest_0.6.27                
[29] Rsamtools_2.8.0               XVector_0.32.0                pkgconfig_2.0.3               htmltools_0.5.2              
[33] MatrixGenerics_1.4.3          dbplyr_2.1.1                  fastmap_1.1.0                 ensembldb_2.16.4             
[37] rlang_0.4.11                  rstudioapi_0.13               RSQLite_2.2.8                 shiny_1.6.0                  
[41] BiocIO_1.2.0                  generics_0.1.0                jsonlite_1.7.2                vroom_1.5.5                  
[45] BiocParallel_1.26.2           dplyr_1.0.7                   RCurl_1.98-1.4                magrittr_2.0.1               
[49] GenomeInfoDbData_1.2.6        Matrix_1.3-4                  Rcpp_1.0.7                    S4Vectors_0.30.0             
[53] fansi_0.5.0                   lifecycle_1.0.0               stringi_1.7.4                 yaml_2.2.1                   
[57] SummarizedExperiment_1.22.0   zlibbioc_1.38.0               BiocFileCache_2.0.0           AnnotationHub_3.0.1          
[61] grid_4.1.0                    blob_1.2.2                    parallel_4.1.0                promises_1.2.0.1             
[65] crayon_1.4.1                  lattice_0.20-44               Biostrings_2.60.2             GenomicFeatures_1.44.2       
[69] hms_1.1.0                     KEGGREST_1.32.0               pillar_1.6.2                  GenomicRanges_1.44.0         
[73] rjson_0.2.20                  biomaRt_2.48.3                stats4_4.1.0                  XML_3.99-0.7                 
[77] glue_1.4.2                    BiocVersion_3.13.1            BiocManager_1.30.16           tzdb_0.1.2                   
[81] png_0.1-7                     vctrs_0.3.8                   httpuv_1.6.3                  purrr_0.3.4                  
[85] assertthat_0.2.1              cachem_1.0.6                  mime_0.11                     xtable_1.8-4                 
[89] restfulr_0.0.13               AnnotationFilter_1.16.0       later_1.3.0                   tibble_3.1.4                 
[93] GenomicAlignments_1.28.0      AnnotationDbi_1.54.1          memoise_2.0.0                 IRanges_2.26.0               
[97] tximport_1.20.0               ellipsis_0.3.2                interactiveDisplayBase_1.30.0
tximeta • 98 views
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Entering edit mode
@mikelove
Last seen 9 hours ago
United States

I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the linkedTxome?

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