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  • cufflinks problems

    Yesterday, I ran cufflinks, and encountered a problem: "Read Type: 0bp single-end", this seemed to have no influence on the result, but when I ran cuffdiff, there was error in the result. From chromosome 1003617-1005575 almost all of the reads's FPKM value are 0, what's wrong?

    Thank you in advance.



    cufflinks -o cufflinks_1 -g xxx.gtf -M xxx_rRNA.gtf -N --min-intron-length 0 ../bowtie-0.12.7/xs.nh.1_mapped.sorted.sam
    cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
    You are using Cufflinks v1.1.0, which is the most recent release.
    [bam_header_read] EOF marker is absent.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    File ../bowtie-0.12.7/xs.nh.1_mapped.sorted.sam doesn't appear to be a valid BAM file, trying SAM...
    [07:14:12] Loading reference annotation.
    [07:14:12] Loading reference annotation.
    [07:14:12] Inspecting reads and determining fragment length distribution.
    > Processed 7122 loci. [*************************] 100%
    > Map Properties:
    > Upper Quartile: 86.00
    > Read Type: 0bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80
    [07:14:14] Assembling transcripts and estimating abundances.
    > Processed 7122 loci. [*************************] 100%

    --------------------------------------------------------------------------------------
    cuffdiff


    cuffdiff -L 1,2,3 -N -M xxx_rRNA.gtf cuffcmp.combined.gtf ../bowtie-0.12.7/xs.nh.1_mapped.sorted.sam ../bowtie-0.12.7/xs.nh.2_mapped.sorted.sam ../bowtie-0.12.7/xs.nh.3_mapped.sorted.sam
    cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff)
    You are using Cufflinks v1.1.0, which is the most recent release.
    [bam_header_read] EOF marker is absent.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    File ../bowtie-0.12.7/xs.nh.1_mapped.sorted.sam doesn't appear to be a valid BAM file, trying SAM...
    [bam_header_read] EOF marker is absent.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    File ../bowtie-0.12.7/xs.nh.2_mapped.sorted.sam doesn't appear to be a valid BAM file, trying SAM...
    [bam_header_read] EOF marker is absent.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    File ../bowtie-0.12.7/xs.nh.3_mapped.sorted.sam doesn't appear to be a valid BAM file, trying SAM...
    [21:31:05] Loading reference annotation.
    [21:31:05] Loading reference annotation.
    [21:31:05] Inspecting maps and determining fragment length distributions.
    > Map Properties:
    > Upper Quartile: 85.00
    > Read Type: 0bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80
    > Map Properties:
    > Upper Quartile: 94.00
    > Read Type: 0bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80
    > Map Properties:
    > Upper Quartile: 111.00
    > Read Type: 0bp single-end
    > Fragment Length Distribution: Truncated Gaussian (default)
    > Default Mean: 200
    > Default Std Dev: 80
    [21:31:13] Modeling fragment count overdispersion.
    [21:31:13] Testing for differential expression and regulation in locus.
    > Processed 7138 loci. [*************************] 100%
    Performed 505 isoform-level transcription difference tests
    Performed 505 tss-level transcription difference tests
    Performed 484 gene-level transcription difference tests
    Performed 0 CDS-level transcription difference tests
    Performed 2 splicing tests
    Performed 38 promoter preference tests
    Performing 0 relative CDS output tests
    Writing isoform-level FPKM tracking
    Writing TSS group-level FPKM tracking
    Writing gene-level FPKM tracking
    Writing CDS-level FPKM tracking


    test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant

    XLOC_003482 XLOC_003482 xxx_ro00918 chr:975490-976618 1 2 OK 1209.76 880.951 -0.457582 0.373318 0.708912 0.897679 no
    3484 XLOC_003483 XLOC_003483 xxx_ro00920 chr:978234-979113 1 2 NOTEST 43.9649 79.511 0.854802 -0.609681 0.542073 1 no
    3485 XLOC_003484 XLOC_003484 xxx_ro00931 chr:979296-998057 1 2 OK 1253.23 1991.14 0.667947 -0.559921 0.575533 0.802329 no
    3486 XLOC_003485 XLOC_003485 xxx_ro00942,xxx_ro00943 chr:1003617-1005575 1 2 NOTEST 0 0 0 0 1 1 no
    3487 XLOC_003486 XLOC_003486 xxx_ro00947 chr:1007721-1007934 1 2 NOTEST 0 0 0 0 1 1 no
    3488 XLOC_003487 XLOC_003487 xxx_ro00948 chr:1007972-1010957 1 2 NOTEST 0 0 0 0 1 1 no
    3489 XLOC_003488 XLOC_003488 xxx_ro00949 chr:1011069-1012488 1 2 NOTEST 0 0 0 0 1 1 no
    3490 XLOC_003489 XLOC_003489 xxx_ro00950 chr:1012490-1013690 1 2 NOTEST 0 0 0 0 1 1 no
    3491 XLOC_003490 XLOC_003490 xxx_ro00951,xxx_ro00952,xxx_ro00953,xxx_ro00954,xxx_ro00955,xxx_ro00956 chr:1013737-1019702 1 2 NOTEST 0 0 0 0 1 1 no
    3492 XLOC_003491 XLOC_003491 xxx_ro00957 chr:1019770-1020169 1 2 NOTEST 0 0 0 0 1 1 no
    3493 XLOC_003492 XLOC_003492 xxx_ro00958 chr:1020214-1022701 1 2 NOTEST 0 0 0 0 1 1 no

  • #2
    I am observing the same 0bp single-end reads being reported by cufflinks.
    I am not sure if this is just a reporting error (that could be safely ignored) or if it is not finding the reads. Any update on this issue yet?

    Comment


    • #3
      Hi, hrajasim

      still can't find a clue, and I tried on Galaxy, also got file like this, frustrated.




      Originally posted by hrajasim View Post
      I am observing the same 0bp single-end reads being reported by cufflinks.
      I am not sure if this is just a reporting error (that could be safely ignored) or if it is not finding the reads. Any update on this issue yet?

      Comment


      • #4
        anybody got the solution ?
        I got same problem too
        Fragment Length Distribution: Truncated Gaussian (default)

        Originally posted by wall_y View Post
        Hi, hrajasim

        still can't find a clue, and I tried on Galaxy, also got file like this, frustrated.

        Comment

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