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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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GENCODE transcriptome v42 not recognised #69

Closed GiBacci closed 1 year ago

GiBacci commented 1 year ago

Hi, I have just mapped my reads against the latest GENCODE human transcriptome (version 42) with Salmon (--gencode option when indexing) but when I import my quant files with tximeta I got this error:

couldn't find matching transcriptome, returning non-ranged SummarizedExperiment

I looked into the meta_info.json file to check the hash and it seems to be correct; I'm posting the content of the file below:

{ "salmon_version": "1.9.0", "samp_type": "none", "opt_type": "vb", "quant_errors": [], "num_libraries": 1, "library_types": [ "U" ], "frag_dist_length": 1001, "frag_length_mean": 23.361253100104336, "frag_length_sd": 6.036313855216654, "seq_bias_correct": false, "gc_bias_correct": false, "num_bias_bins": 4096, "mapping_type": "mapping", "keep_duplicates": false, "num_valid_targets": 251550, "num_decoy_targets": 194, "num_eq_classes": 111, "serialized_eq_classes": false, "eq_class_properties": [ "range_factorized", "gzipped" ], "length_classes": [ 549, 772, 1395, 2643, 347561 ], "index_seq_hash": "adf85ccb8ecd0dd263461e763872a802ae20f0258a96e4dc95506c36de54d9a7", "index_name_hash": "f0dc84141a658e75c3a77ce593b599b401b98f79c18efbd62484901f7d62bb3f", "index_seq_hash512": "aed780be81faf3d7e60a111ccdb6c5d9210efc13245431849dd69b898c969b43b48e08b403bbb28298959c0dea42987eb2f701ae472b8b796b748be496534abb", "index_name_hash512": "e860b9f24f60a391d94422283c9d156dfde95d972e31ee7a56c2b1fcf5e115af353675305610e7037708def8b73afe7c5ac6f47cfff2d32f64441fc54e8481aa", "index_decoy_seq_hash": "b87b7a94564c31d78da407e60a0aeb310b2dbdb398e0ddb39392286aaf2fe88c", "index_decoy_name_hash": "5fc84a462ccf4735efdc48604a520ee47e1319156c2a5c252f5daba1e99bb401", "num_bootstraps": 0, "num_processed": 9400118, "num_mapped": 33367, "num_decoy_fragments": 516, "num_dovetail_fragments": 0, "num_fragments_filtered_vm": 520, "num_alignments_below_threshold_for_mapped_fragments_vm": 560, "percent_mapped": 0.3549636291799741, "call": "quant", "start_time": "Fri Nov 18 11:23:10 2022", "end_time": "Fri Nov 18 11:23:51 2022" }

I cannot figure out what I'm doing wrong...

Thanks in advance, Giovanni

Session Info:

R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6

Matrix products: default 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] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[7] tibble_3.1.6 ggplot2_3.3.5 tidyverse_1.3.1 tximeta_1.10.0

loaded via a namespace (and not attached): [1] colorspace_2.0-3 rjson_0.2.21 ellipsis_0.3.2
[4] XVector_0.32.0 fs_1.5.2 GenomicRanges_1.44.0
[7] rstudioapi_0.13 bit64_4.0.5 interactiveDisplayBase_1.30.0 [10] AnnotationDbi_1.54.1 fansi_1.0.2 lubridate_1.8.0
[13] xml2_1.3.3 tximport_1.20.0 cachem_1.0.6
[16] knitr_1.37 jsonlite_1.8.0 Rsamtools_2.8.0
[19] broom_0.7.12 dbplyr_2.1.1 png_0.1-7
[22] shiny_1.7.3 BiocManager_1.30.16 compiler_4.1.0
[25] httr_1.4.2 backports_1.4.1 assertthat_0.2.1
[28] Matrix_1.4-0 fastmap_1.1.0 lazyeval_0.2.2
[31] cli_3.2.0 later_1.3.0 htmltools_0.5.2
[34] prettyunits_1.1.1 tools_4.1.0 gtable_0.3.0
[37] glue_1.6.2 GenomeInfoDbData_1.2.6 rappdirs_0.3.3
[40] Rcpp_1.0.8.2 Biobase_2.52.0 cellranger_1.1.0
[43] vctrs_0.3.8 Biostrings_2.60.2 rtracklayer_1.52.1
[46] xfun_0.30 rvest_1.0.2 mime_0.12
[49] lifecycle_1.0.1 restfulr_0.0.15 ensembldb_2.16.4
[52] XML_3.99-0.9 AnnotationHub_3.0.2 zlibbioc_1.38.0
[55] scales_1.1.1 vroom_1.5.7 hms_1.1.1
[58] promises_1.2.0.1 MatrixGenerics_1.4.3 ProtGenerics_1.24.0
[61] parallel_4.1.0 SummarizedExperiment_1.22.0 AnnotationFilter_1.16.0
[64] yaml_2.3.5 curl_4.3.2 memoise_2.0.1
[67] biomaRt_2.48.3 stringi_1.7.6 RSQLite_2.2.10
[70] BiocVersion_3.13.1 S4Vectors_0.30.2 BiocIO_1.2.0
[73] GenomicFeatures_1.44.2 BiocGenerics_0.38.0 filelock_1.0.2
[76] BiocParallel_1.26.2 GenomeInfoDb_1.28.4 rlang_1.0.2
[79] pkgconfig_2.0.3 matrixStats_0.61.0 bitops_1.0-7
[82] evaluate_0.15 lattice_0.20-45 GenomicAlignments_1.28.0
[85] bit_4.0.4 tidyselect_1.1.2 magrittr_2.0.2
[88] R6_2.5.1 IRanges_2.26.0 generics_0.1.2
[91] DelayedArray_0.18.0 DBI_1.1.2 withr_2.5.0
[94] pillar_1.7.0 haven_2.4.3 KEGGREST_1.32.0
[97] RCurl_1.98-1.6 modelr_0.1.8 crayon_1.5.0
[100] utf8_1.2.2 BiocFileCache_2.0.0 tzdb_0.2.0
[103] rmarkdown_2.13 progress_1.2.2 grid_4.1.0
[106] readxl_1.3.1 blob_1.2.2 reprex_2.0.1
[109] digest_0.6.29 xtable_1.8-4 httpuv_1.6.6
[112] stats4_4.1.0 munsell_0.5.0

mikelove commented 1 year ago

You are using a version of tximeta that predates that version of Gencode. You can just install the latest from github, install_github("mikelove/tximeta") or you can update to newer R/Bioc.