Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • summarizeOverlaps too, too slow then freeze

    I hope someone can help in this issue.


    I have 8 bam files from mm9 alignment, each ~4-5 geg in size. When I run summarizeOverlaps over 3 files, it takes 2-3 hours to finish and it works although my computer almost freezes up. But when I put the 8 files together, then keep it on overnight (as it takes too long to wait), the computer freezes (although it is 16 geg i7 mac, so supposed to be powerful) and the command never results in anything.

    I am making my own txdb file from gtf that I used for the alignment to match the naming of the chromosomes. (script is below).

    Do you have any tips on how I can get the summzerOverlaps to work on the 8 files to create one se file without freezing up the computer? I have been trying to do that for the past 2 week and always same result.


    Any input is appreciated.

    here’s the script:


    library("DESeq2")
    library("GenomicFeatures")
    library("Rsamtools")
    library("GenomicAlignments")
    library("GenomicRanges”)

    mm9_from_cluster_gtf_txdb <- makeTranscriptDbFromGFF(file="~/Desktop/genes.gtf", format="gtf”)
    head(seqlevels(mm9_from_cluster_gtf_txdb))
    saveDb(mm9_from_cluster_gtf_txdb, file="/Path/To/Libraries/TxDB/mm9_from_cluster_Ensembl_txdb.sqlite”)
    exonsByGene<-exonsBy(mm9_from_cluster_gtf_txdb,by="gene")
    seqinfo(exonsByGene)

    fls <- list.files("/Path/To/BamFiles", pattern="paired.accepted_hits.bam", full= TRUE)
    fls

    Experiment <- c(fls[2:8], fls[1])
    Experiment

    bamLst_experiment <- BamFileList(Experiment, yieldSize=100000)
    seqinfo(bamLst_experiment)

    se_test_experiment <- summarizeOverlaps(exonsByGene,bamLst_experiment, mode="Union", singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE) <<<This is the step that freezes the computer when I run the 8 of the files together.
    Last edited by habbas; 12-29-2014, 02:37 PM.

  • #2
    Habbas

    are you using the most recent versions of R and the packages?
    See http://www.bioconductor.org/packages...lignments.html (version 1.2.1) and in fact I would even try R-devel and http://www.bioconductor.org/packages...lignments.html (version 1.3.19).

    If the problem persists, I recommend contacting the maintainer of the "GenomicAlignments" package (which contains summarizeOverlaps) directly, possibly via the Bioconductor forum.

    Kind regards
    Wolfgang
    Wolfgang Huber
    EMBL

    Comment


    • #3
      Thank you for your reply. I am using the latest R version. I am not sure what's the difference between the two links you provided above. They both seem to link to the same downloadable links:

      source("http://bioconductor.org/biocLite.R")
      biocLite("GenomicAlignments")

      Is there a way to have a link to the R-devel version so i could try it? I even tried running the same thing over 30 hours. It looked like it was consuming memory (~600 megabyte ram) but it still took 30 hours without any results.

      Comment


      • #4
        Here's my sessionInfo(). Does it look right?

        R version 3.1.2 (2014-10-31)
        Platform: x86_64-apple-darwin13.4.0 (64-bit)

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

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

        other attached packages:
        [1] GenomicAlignments_1.2.0 Rsamtools_1.18.1 Biostrings_2.34.0 XVector_0.6.0
        [5] GenomicRanges_1.18.3 GenomeInfoDb_1.2.2 IRanges_2.0.0 S4Vectors_0.4.0
        [9] BiocGenerics_0.12.0 BiocInstaller_1.16.1

        loaded via a namespace (and not attached):
        [1] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 BiocParallel_1.0.0 bitops_1.0-6
        [6] brew_1.0-6 checkmate_1.5.0 codetools_0.2-9 DBI_0.3.1 digest_0.6.4
        [11] fail_1.2 foreach_1.4.2 iterators_1.0.7 RSQLite_1.0.0 sendmailR_1.2-1
        [16] stringr_0.6.2 tools_3.1.2 zlibbioc_1.12.0

        Comment


        • #5
          I posted the question on the support website of bioconductor and found a solution for the problem. Here's the link for it:

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM
          • seqadmin
            Recent Advances in Sequencing Analysis Tools
            by seqadmin


            The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
            05-06-2024, 07:48 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Today, 01:32 PM
          0 responses
          8 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-24-2024, 07:15 AM
          0 responses
          199 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 10:28 AM
          0 responses
          220 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 05-23-2024, 07:35 AM
          0 responses
          230 views
          0 likes
          Last Post seqadmin  
          Working...
          X