I have an issue using
tximport with kallisto output. I never had this issue before, and I can't figure out why it is happening. When applying it on a large dataset (over 3000 transcriptome mapped cells from single-cell RNAseq data), some genes from a subset of the cells (1/4 of the cells) have
NA values. When I checked the counts of these genes in the corresponding
abundance.tsv files, some of them seem to be expressed at high levels (around 1000 counts). Many of these genes also have only 1 transcript.
The code I'm running is the following:
txi <- tximport(files = abundance.files, type = "kallisto", tx2gene = tx2gene, importer = read_tsv)
I also tried importing with
rhdf5, and it didn't change in anything.
sessionInfo() is the following:
sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib locale:  C attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  readr_1.1.1 tximport_1.4.0 magrittr_1.5 loaded via a namespace (and not attached):  zlibbioc_1.22.0 compiler_3.4.1 plyr_1.8.4 R6_2.2.2 hms_0.3 tools_3.4.1  rhdf5_2.20.0 reshape2_1.4.2 tibble_1.3.4 Rcpp_0.12.13 stringi_1.1.5 stringr_1.2.0  rlang_0.1.4
Any help to fix this issue is highly appreciated!
Thanks for your help!