Hi, 

I am using the QuasR package to analyse my RNASEQ data. when I run qAlign using bowtie, it works but when I rather use the spliceMap I got this error message "failed while sorting 25mer-alignments". I read all the literature I could find on QuasR and I have not been able to figure out how to fix this problem. Does someone Have I idea what causing this error

thank you

Hi Hans_Rudolf, 

1- my read length is 36 pb 

3- session info: I am pasting all the session info a got in from R

R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Rsubread_1.20.2                         ShortRead_1.28.0                        GenomicAlignments_1.6.1                
 [4] SummarizedExperiment_1.0.1              Rsamtools_1.22.0                        BiocParallel_1.4.0                     
 [7] SRAdb_1.28.0                            RCurl_1.95-4.7                          bitops_1.0-6                           
[10] graph_1.48.0                            BiocInstaller_1.20.1                    org.Hs.eg.db_3.2.3                     
[13] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.22.5                  AnnotationDbi_1.32.0                   
[16] Biobase_2.30.0                          BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.38.0                        
[19] rtracklayer_1.30.1                      Biostrings_2.38.2                       XVector_0.10.0                         
[22] QuasR_1.10.0                            Rbowtie_1.10.0                          GenomicRanges_1.22.1                   
[25] GenomeInfoDb_1.6.1                      IRanges_2.4.4                           S4Vectors_0.8.3                        
[28] BiocGenerics_0.16.1                     RSQLite_1.0.0                           DBI_0.3.1                              

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2          RColorBrewer_1.1-2   futile.logger_1.4.1  plyr_1.8.3           futile.options_1.0.0
 [6] GenomicFiles_1.6.0   tools_3.2.2          zlibbioc_1.16.0      biomaRt_2.26.1       digest_0.6.8        
[11] lattice_0.20-33      gtable_0.1.2         GEOquery_2.36.0      proto_0.3-10         hwriter_1.3.2       
[16] stringr_1.0.0        grid_3.2.2           XML_3.98-1.3         latticeExtra_0.6-26  ggplot2_1.0.1       
[21] reshape2_1.4.1       lambda.r_1.1.7       magrittr_1.5         scales_0.3.0         MASS_7.3-45         
[26] colorspace_1.2-6     stringi_1.0-1        munsell_0.4.2      

however I don't know what do you mean exactly by auxiliary file but I don't think I using any

Thank you 

Nadia

Hi Nadia

The QuasR tool qAlign has an option "auxiliaryFile" which allows you to align your reads in addition to the genome to other auxiliary files to check for spike-ins, contamination, etc.

But let's go back to your original question:  The problem is the rather short read length of only 36nts. SpliceMap struggles with reads shorter than 50nts. See the original reference for more details (Au KF, Jiang H, Lin L, Xing Y and Wong WH (2010). “Detection of splice junctions from paired-end RNA-seq data by SpliceMap.” Nucleic Acids Research, 38(14), pp. 4570–4578. http://nar.oxfordjournals.org/content/38/14/4570.full )

Regards, Hans-Rudolf