Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Importing SAM Files in Megan Julian1988 Bioinformatics 2 05-21-2015 02:24 AM
importing sam files from bowtie to megan werbner Bioinformatics 0 01-20-2015 03:14 AM
sam files convert to bam files error awayihaha Bioinformatics 7 03-11-2014 09:03 AM
cuffdiff error on mixed tophat1 &2 .bam files hooperj RNA Sequencing 0 01-20-2013 04:12 PM
Problem importing BAM files in Artemis pasta Bioinformatics 7 01-31-2012 05:26 AM

Thread Tools
Old 06-26-2015, 10:00 AM   #1
Location: Southampton

Join Date: Jun 2015
Posts: 36
Default simpleRNASeq error importing BAM files

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?

> 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

[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
ea11 is offline   Reply With Quote

error, simplernaseq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 03:17 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO