SpiliceMap processing time

Question

[tarek.mohamed]

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 fastq 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 alignment. I run the alignment 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

[jomo018]

Suggest you start with a short 100k read fastq file and calculate the required timefor the full input. Also provide cpu and dram information.