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  • adrian
    replied
    sorry for bumping this.
    Tophat/cufflinks experts - appreciate your opinion, ideas/suggestions.
    thanks
    adrian

    Leave a comment:


  • adrian
    replied
    I forgot to mention,
    I have many differentially expressed genes and spliceforms, I am not sure to believe them or not!
    Adrian

    Leave a comment:


  • adrian
    started a topic cuffcompare - wrong results

    cuffcompare - wrong results

    Hi:
    I did following:

    cuffcompare -i gtf_out_list -r /UCSC/hg19/Annotation/Genes/genes.gtf


    cut -f4 cuffcmp.tracking | sort | uniq -c
    40816 =
    20 c

    As per cuffcompare manual column 5 is listed as code column, however I see codes in column 4.

    Also my other MAIN concern is why I have over 40K '=' and very little C and no other codes.

    Is something wrong with my cufflinks, cuffmerge and cuffdiff?

    I also checked same with individual .tmap files:
    cut -f3 cuffcmp.transcripts.gtf.tmap | sort | uniq -c
    40868 =
    20 c
    1 class_code


    my refmap file is empty.


    Could any one suggest what could be wrong. I have been struggling with this for last 4 months and I think I cant get past of this. I request your help.

    Thanks
    Adrian




    The following is what I did :

    ### TOPHAT ###
    tophat2 --b2-fast -p 16 -r 200
    -G genes.gtf
    UCSC/hg19/Sequence/Bowtie2Index/genome/
    -o out
    r1.fastq r2.fastq


    #### CUFFLINKS #####

    cufflinks -p 8 -N -o CLRes
    -G genes.gtf
    -b UCSC/hg19/Sequence/Bowtie2Index/genome.fa
    -M rrna.gtf (this includes rrna and trna)
    -u
    accepted_hits.bam


    ####CUFFMERGE ####

    cuffmerge -p 16 -o CMergeOut
    -g genes.gtf
    -s UCSC/hg19/Sequence/Bowtie2Index/genome.fa
    runs_list

    cuffdiff:
    cuffdiff -p 12 -o cuffdiffOut

    -N
    -u

    -b UCSC/hg19/Sequence/Bowtie2Index/genome.fa
    -M rrna.gtf (this includes rrna and trna)

    -L samp1,samp2,samp3

    s11.bam,s12.bam,s13.bam s21.bam,s22.bam,s23.bam s31.bam,s32.bam,s33.bam

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