Dear All,
I'm new to RNA-Seq and Bioinformatics. We have done a RNA-Seq study using Illumina Hi-Seq (paired-end, 90bp reads) on two cell types.
I have managed to remove the adapters, trim low quality reads and remove reads < 50bp (Trim Galore). I have then mapped them (TopHat-v2.0.8b) and assembled the mapped reads (Cufflinks).
Is there a way to sort the transcripts.gtf file based on fpkm values to look for the top 100 highly expressed genes? (to make sure that the house-keeping genes/ genes that we know to be highly expressed are indeed highly expressed)
Any help would be much appreciated!
Cheers!
I'm new to RNA-Seq and Bioinformatics. We have done a RNA-Seq study using Illumina Hi-Seq (paired-end, 90bp reads) on two cell types.
I have managed to remove the adapters, trim low quality reads and remove reads < 50bp (Trim Galore). I have then mapped them (TopHat-v2.0.8b) and assembled the mapped reads (Cufflinks).
Is there a way to sort the transcripts.gtf file based on fpkm values to look for the top 100 highly expressed genes? (to make sure that the house-keeping genes/ genes that we know to be highly expressed are indeed highly expressed)
Any help would be much appreciated!
Cheers!
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