Question: SpiliceMap processing time
gravatar for tarek.mohamed
4.7 years ago by
tarek.mohamed270 wrote:

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:
Performing genomic alignments for 12 samples. See progress in the log file:
E:/Doxorubicin Project RNA-seq Data\QuasR_log_1b4c68073cc5.txt

rna-seq splicemap quasr • 998 views
ADD COMMENTlink written 4.7 years ago by tarek.mohamed270
Suggest you start with a short 100k read fastq file and calculate the required timefor the full input. Also provide cpu and dram information.
ADD REPLYlink written 4.7 years ago by jomo018610
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