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  • [ABySS] Odd histogram of mate-paired reads

    Dear,

    I try to assemble a genome with 2 paired-end sets (300, 500) and 2 mate-pair sets (2K, 5K).

    The insert size histograms, the intermediate results of ABySS (1.2.5), shows odd distribution of insert size.

    Paired-end sets show reasonable peaks, however the peaks of the mate-pair sets are placed between 0 to 500.

    To check the mate-pair reads, I estimated the insert size by mapping them to a reference genome. And we confirmed that almost of the reads were mapped within reasonable range.

    I think that ABySS may not predict insert size for mate-pair reads.

    I need your comments.

    P.s.) The plot of the histograms is attached. Please refer it.
    Attached Files

  • #2
    Originally posted by wonhyong.chung View Post
    Dear,

    I try to assemble a genome with 2 paired-end sets (300, 500) and 2 mate-pair sets (2K, 5K).

    The insert size histograms, the intermediate results of ABySS (1.2.5), shows odd distribution of insert size.

    Paired-end sets show reasonable peaks, however the peaks of the mate-pair sets are placed between 0 to 500.

    To check the mate-pair reads, I estimated the insert size by mapping them to a reference genome. And we confirmed that almost of the reads were mapped within reasonable range.

    I think that ABySS may not predict insert size for mate-pair reads.

    I need your comments.

    P.s.) The plot of the histograms is attached. Please refer it.
    To do these estimation, reads are aligned to preliminary contigs. Maybe none of them are longer than 2k.

    I encourage you to try Ray (I am the author).



    Running Ray is simple:

    Code:
    mpirun -np 32 Ray -k31 \
    -p 300_1.fastq 300_2.fastq \
    -p 500_1.fastq 500_2.fastq \
    -p 2k_1.fastq 2k_2.fastq \
    -p 5k_1.fastq 5k_5.fastq \
    -o test-ray
    
    less test-ray.LibraryStatistics.txt

    Comment


    • #3
      Thanks for your advice.

      I'll post again after trying Ray.

      Comment

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