Hi all,

I am relatively new to RNA-seq analysis and using R and bioconductor and would like some help.
I have some aligned BAM files that have been aligned, and I am looking to create count tables from the aligned files using simpleRNASeq. However, I am getting an error when it comes to getting in the BAM files into R.

Below is the script I'm using and the resulting error:

> library(easyRNASeq)
> setwd("G:/RNA-seq data/bam/")
> filenames <- dir()
> bf <- getBamFileList(filenames)

Warning message:
In getBamFileList(filenames) :
You either have provided BAM index files (.bai) as part of the filenames argument or your pattern matched BAM index files! Removing these from the files list to process.

I'm not really understanding the error. The BAI files are in the same folder and the corresponding BAM files after I used Rsamtools to index the BAM files. Therefore I can't seem to find anything wrong.

Can anyone please help?
Thanks,


> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252

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

other attached packages:
[1] easyRNASeq_2.2.1 BiocInstaller_1.16.5

loaded via a namespace (and not attached):
[1] annotate_1.44.0 AnnotationDbi_1.28.2 base64enc_0.1-2 BatchJobs_1.6 BBmisc_1.9 Biobase_2.26.0 BiocGenerics_0.12.1 BiocParallel_1.0.3
[9] biomaRt_2.22.0 Biostrings_2.34.1 bitops_1.0-6 brew_1.0-6 checkmate_1.6.0 codetools_0.2-11 DBI_0.3.1 DESeq_1.18.0
[17] digest_0.6.8 edgeR_3.8.6 fail_1.2 foreach_1.4.2 genefilter_1.48.1 geneplotter_1.44.0 GenomeInfoDb_1.2.5 genomeIntervals_1.22.3
[25] GenomicAlignments_1.2.2 GenomicRanges_1.18.4 grid_3.1.3 hwriter_1.3.2 intervals_0.15.0 IRanges_2.0.1 iterators_1.0.7 lattice_0.20-31
[33] latticeExtra_0.6-26 limma_3.22.7 LSD_3.0 magrittr_1.5 parallel_3.1.3 RColorBrewer_1.1-2 RCurl_1.95-4.6 Rsamtools_1.18.3
[41] RSQLite_1.0.0 S4Vectors_0.4.0 sendmailR_1.2-1 ShortRead_1.24.0 splines_3.1.3 stats4_3.1.3 stringi_0.5-2 stringr_1.0.0
[49] survival_2.38-2 tools_3.1.3 XML_3.98-1.2 xtable_1.7-4 XVector_0.6.0 zlibbioc_1.12.0

Here is the warning message:

Warning message:
In getBamFileList(filenames) :
You either have provided BAM index files (.bai) as part of the filenames argument or your pattern matched BAM index files! Removing these from the files list to process.

This is trying to indicate to you that your filenames includes both the BAM files as well as the index files associated with those BAM files, and that you are only supposed to be supplying the BAM files alone. You want to do something like

filenames2 <- dir(".", "bam$")

Compare filenames2 to filenames to see the difference.