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  • how to provide parameters for 4 replicates to cuffdiff

    It is not clear how to provide parameters to cuffcompare/cuffdiff to determine differential gene expression using 4 replicates in each condition.

    Usage:
    cuffcompare [-r <reference_mrna.gtf>] [-R] [-T] [-V] [-s <seq_path>]
    [-o <stats.txt>] [-p <cprefix>]
    {-i <input_gtf_list> | <input1.gtf> [<input2.gtf> .. <inputN.

    How do I indicate that the first 4 gtf files are for condition 1 and the next 4 are for condition 2? or cuffcompare is smart enough to figure this out?

    Similarly for cuffdiff, how does one indicate that the first 4 sam files are from different condition than the next 4? What if I want to compare 3 verus 4?

    Usage: cuffdiff [options] <transcripts.gtf> <sample1_hits.sam> <sample2_hits.sam> [... sampleN_hits.sam]
    Supply replicate SAMs as comma separated lists for each condition: sample1_rep1.sam,sample1_rep2.sam,...sample1_repM.sam

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