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  • graham.hamilton
    Junior Member
    • May 2010
    • 1
    #1

    Cufdiff2 problems

    Hi

    I am analysing RNA-Seq data using the Tophat2/Cufflinks2(Cuffdiff2) pipeline. This has worked well for several projects, however for this project I am only getting differentially expressed genes output if I omit the fragment length bias correction step.
    I have run the Tophat2 output through Cuffdiff v1.3.0 with fragment length bias correction on and the program output significantly expressed genes.
    Blow is the command I would like to run
    cuffdiff2 -o bombyx_tophat2_cuffdiff2_out -b /data2/genomes/bowtie2_indexes/B_mori/B_mori.fa -p 12 -L anterior,posterior -u /data2/genomes/bowtie2_indexes/B_mori/Annotation/B_mori.gff /data2/graham/julian_dow/bombyx/FC052_s1_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s4_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s5_tophat2_Bm/accepted_hits.bam /data2/graham/julian_dow/bombyx/FC052_s6_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s7_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s8_tophat2_Bm/accepted_hits.bam

    But I have to run this command to get any significant genes
    cuffdiff2 -o bombyx_tophat2_cuffdiff2_out -p 12 -L anterior,posterior -u /data2/genomes/bowtie2_indexes/B_mori/Annotation/B_mori.gff /data2/graham/julian_dow/bombyx/FC052_s1_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s4_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s5_tophat2_Bm/accepted_hits.bam /data2/graham/julian_dow/bombyx/FC052_s6_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s7_tophat2_Bm/accepted_hits.bam,/data2/graham/julian_dow/bombyx/FC052_s8_tophat2_Bm/accepted_hits.bam

    Can anyone tell me why this is happening?

    Graham
    Tags: bioinformatic analysis, cuffdiff 2, rna sequencing
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