RNAseq_alignment_SpliceMap processing time_QuasR
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@tarekmohamed-9489
Last seen 5.2 years ago

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

 

SpliceMap QuasR RNAseq Alignment • 1.5k views
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@hotz-hans-rudolf-3951
Last seen 3.5 years ago
Switzerland

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

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Dear Hans,

I have access to the university server.

In your opinion, how many computer nodes and processor do I need to perform this analysis?

Thanks

Tarek

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Hi Tarek

simple answer: the more the better (i.e faster). Though, it all depends on your server and its storage set-up and 'more' does not always mean faster. So, I suggest you better ask this question your IT deartment.

Hans-Rudolf

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