I have Cufflink generated .gtf files on 2 different Rna-seq datasets , each belonging to a different tissue.
ex: adrenal1 and adrenal2 datasets ex: brain 1 and brain 2 datasets.
i need to analyse DGE : differential gene expression between the 2 samples that is between adrenal and brain tissue.
Am i supposed to add the .gtf files of both tissues together for cuffmerge??
pls see the snapshot : http://s31.postimg.org/bfwh37ofv/biostar_cuffmerge.jpg
4 answers
See here, under the common uses of the Cufflinks packages. Yes, it's common to merge the two transcriptomic GTF files, if you want them to be quantified in all your samples. Say sample i from one of your brain samples has a transcript discovered in cufflinks that isn't in any of your other samples, you'd need to quantify it in all samples post cufflinks - hence the reason for the CuffMerge.
thanks Andrew
what if there are more 2 rna seq samples from the same tissue ??
like 2 samples (adrenal1.fastq and adrenal2.fastq) and (brain1.fastq and brain2.fastq) and we need to know the differential expression between the samples? so all the 4 files are to be merged for cufflinks at a time?
thanks SUKHDEEP SINGH
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Changed your question heading to a more detailed one!