Recently,I'm using Cufflinks to process my RNA-seq data,and I have 4 tissues(more than two).In the mannual of cuffdiff,you said,if more than two are provided, Cuffdiff tests for differential expression and regulation between all pairs of samples. But when I used the cuffdiff,it only report one pairs of samples.There was only one gene_exp.diff in the output directory.Command was just as below,
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cuffdiff -o DEG_cuffdiff -p 20 cuffcmp.combined.gtf ./tophat_sd/accepted_hits.bam ./tophat_em/accepted_hits.bam tophat_en1/accepted_hits.bam ./tophat_en2/accepted_hits.bam
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What's my problem in using cuffdiff?
Also I want to compare gene expression of duplicate gene pairs, and is it neccesery to remove the reads that mapped to multiple location in the BAM file generated by Tophat as duplicate gene pairs have high sequence similarity ?
Thanks!
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cuffdiff -o DEG_cuffdiff -p 20 cuffcmp.combined.gtf ./tophat_sd/accepted_hits.bam ./tophat_em/accepted_hits.bam tophat_en1/accepted_hits.bam ./tophat_en2/accepted_hits.bam
======================================
What's my problem in using cuffdiff?
Also I want to compare gene expression of duplicate gene pairs, and is it neccesery to remove the reads that mapped to multiple location in the BAM file generated by Tophat as duplicate gene pairs have high sequence similarity ?
Thanks!
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