Error in CountPeaks step about sierra

[johnchamberlin]

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /uufs/chpc.utah.edu/sys/installdir/intel/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin/libmkl_intel_lp64.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] stats graphics grDevices utils datasets methods base

other attached packages:
[1] Sierra_0.99.27

loaded via a namespace (and not attached):
[1] ProtGenerics_1.20.0 bitops_1.0-6
[3] matrixStats_0.56.0 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.2
[7] httr_1.4.1 GenomeInfoDb_1.24.2
[9] tools_4.0.2 backports_1.1.8
[11] R6_2.4.1 rpart_4.1-15
[13] lazyeval_0.2.2 Hmisc_4.4-0
[15] DBI_1.1.0 BiocGenerics_0.34.0
[17] Gviz_1.32.0 colorspace_1.4-1
[19] nnet_7.3-14 tidyselect_1.1.0
[21] gridExtra_2.3 prettyunits_1.1.1
[23] bit_1.1-15.2 curl_4.3
[25] compiler_4.0.2 Biobase_2.48.0
[27] htmlTable_2.0.1 DelayedArray_0.14.0
[29] rtracklayer_1.48.0 scales_1.1.1
[31] checkmate_2.0.0 genefilter_1.70.0
[33] askpass_1.1 rappdirs_0.3.1
[35] stringr_1.4.0 digest_0.6.25
[37] Rsamtools_2.4.0 foreign_0.8-80
[39] XVector_0.28.0 dichromat_2.0-0
[41] base64enc_0.1-3 jpeg_0.1-8.1
[43] pkgconfig_2.0.3 htmltools_0.5.0
[45] ensembldb_2.12.1 dbplyr_1.4.4
[47] BSgenome_1.56.0 htmlwidgets_1.5.1
[49] rlang_0.4.7 rstudioapi_0.11
[51] RSQLite_2.2.0 generics_0.0.2
[53] BiocParallel_1.22.0 acepack_1.4.1
[55] dplyr_1.0.0 VariantAnnotation_1.34.0
[57] RCurl_1.98-1.2 magrittr_1.5
[59] GenomeInfoDbData_1.2.3 Formula_1.2-3
[61] Matrix_1.2-18 Rcpp_1.0.5
[63] munsell_0.5.0 S4Vectors_0.26.1
[65] lifecycle_0.2.0 stringi_1.4.6
[67] SummarizedExperiment_1.18.2 zlibbioc_1.34.0
[69] BiocFileCache_1.12.0 grid_4.0.2
[71] blob_1.2.1 parallel_4.0.2
[73] crayon_1.3.4 lattice_0.20-41
[75] Biostrings_2.56.0 splines_4.0.2
[77] annotate_1.66.0 GenomicFeatures_1.40.1
[79] hms_0.5.3 knitr_1.33
[81] pillar_1.4.6 GenomicRanges_1.40.0
[83] codetools_0.2-16 biomaRt_2.44.1
[85] stats4_4.0.2 XML_3.99-0.4
[87] glue_1.4.1 biovizBase_1.36.0
[89] latticeExtra_0.6-29 data.table_1.12.8
[91] foreach_1.5.0 png_0.1-7
[93] vctrs_0.3.1 gtable_0.3.0
[95] openssl_1.4.2 purrr_0.3.4
[97] assertthat_0.2.1 ggplot2_3.3.2
[99] xfun_0.24 xtable_1.8-4
[101] AnnotationFilter_1.12.0 survival_3.1-12
[103] SingleCellExperiment_1.10.1 tibble_3.0.3
[105] iterators_1.0.12 GenomicAlignments_1.24.0
[107] AnnotationDbi_1.50.1 memoise_1.1.0
[109] IRanges_2.22.2 cluster_2.1.0
[111] ellipsis_0.3.1

[johnchamberlin]

I suspect the problem is that the CB and UMI tags were not included in the STARsolo outputted bam. (--outSAMattributes ... option was omitted, defaults to no tags in BAM). I'll reopen if this doesn't fix it. thanks,