Hi All,

I am analyzing RNAseq data for 12 samples with and without treatment performed on  Hiseq illumina platform ( paired end ,100 bp reads, 40 million reads / sample) quality of fastaq files is fine. At this step, I am interested in DGE rather than splicing data. I am using QuasR to perform RNA-seq data alignment, QuasR is using Splicemap for alignmet. I run the alignmet and after 7 days I did not a single file done. Any advice to increase the speed ( I am using my own PC).

>proj_SpliceMap <- qAlign(sampleFile, genomeFile,splicedAlignment=TRUE,cacheDir = "E:/Doxorubicin Project RNA-seq Data")

alignment files missing - need to:
    create 12 genomic alignment(s)
will start in ..9s..8s..7s..6s..5s..4s..3s..2s..1s
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
FSMMJ02UCX1 
          1 
Performing genomic alignments for 12 samples. See progress in the log file:
E:/Doxorubicin Project RNA-seq Data\QuasR_log_1b4c68073cc5.txt

Hi Tarek

I don't know what the architecture looks like for your pc, but have you tried to work with a  cluster object (to enable parallel processing) as suggested in the QuasR vignette?

Though you probably just have to look for bigger compute resources.

Hans-Rudolf