Cufflinks - top 100 genes

[reuben.jacob]

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!

[GenoMax]

It is not clear if you are using a known GTF file. If you only want to see the top 100 genes then you could use a read counting program like featureCounts to get real counts for your samples.

But if you just want to quickly see FPKM values in transcript.gtf files from cufflinks then try this. High FPKM values will be at the end of the display.

$ cut -f 9 transcripts.gtf | awk -F'"' '{print $2,"\t", $8}' | uniq | sort -s -k2n

[reuben.jacob]

Sorry for the late reply! Thank you very much GenoMax! I just used the code and its what I needed. Really appreciate it! Cheers

[GenoMax]

You are welcome. Thanks for the confirmation that the code worked.