I have 2 RNA-Seq biological replicates and I ran Tophat and then Cufflinks on it separately for both samples. The outputs of Cufflinks for each replicates are:
Replicate 1:
1. transcript.gtf file
2. genes.fpkm_tracking
3. isoform.fpkm_tracking
Replicate 2:
1. transcript.gtf file
2. genes.fpkm_tracking
3. isoform.fpkm_tracking
I would like to compare the differential expression between the two biological replicates by running CuffDiff. So, my question is when I am running the following command:
cuffdiff [options]* <transcripts.gtf> <sample1_replicate1.sam[,...,sample1_replicateM]> <sample2_replicate1.sam[,...,sample2_replicateM.sam]>... [sampleN.sam_replicate1.sam[,...,sample2_replicateM.sam]]
What should be my transcripts.gtf file ? Is it the combination of the two transcripts.gtf files or is it of replicate 1/2 ?
Thanks.
Replicate 1:
1. transcript.gtf file
2. genes.fpkm_tracking
3. isoform.fpkm_tracking
Replicate 2:
1. transcript.gtf file
2. genes.fpkm_tracking
3. isoform.fpkm_tracking
I would like to compare the differential expression between the two biological replicates by running CuffDiff. So, my question is when I am running the following command:
cuffdiff [options]* <transcripts.gtf> <sample1_replicate1.sam[,...,sample1_replicateM]> <sample2_replicate1.sam[,...,sample2_replicateM.sam]>... [sampleN.sam_replicate1.sam[,...,sample2_replicateM.sam]]
What should be my transcripts.gtf file ? Is it the combination of the two transcripts.gtf files or is it of replicate 1/2 ?
Thanks.
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