Hi all,
I run cuffdiff on my control vs condition to check if the mRNA expression of the gene I've knocked-down (from Hela cells) is lower than the mRNA expression of my control.
Gladly I saw that indeed the knock-down sample expresses lower FPKM values of that specific gene. great.
However, I notice very high values of some microRNA:
NR_106781 has a value of 1,460,000
NR_039666 has a value of 995,697
NR_039828 & NR_002574 & NR_037428 are around 15,000
and around 15 more tracks are above 4000
the command line I used:
cuffdiff -p 6 -b hg19/fasta/ -u --no-update-check -v -L control,condition -o /cuffdiff hg19refseq.gtf control/accepted_hits.bam condition/accepted_hits.bam
* I used Refseq hg19 downloaded from UCSC table browser
So these results obviously raises question:
Why those MicroRNA FPKM are so high ?
And how could FPKM values be over million considering that FPKM stands for fragments per kilo per million ?
Anyone ?
I run cuffdiff on my control vs condition to check if the mRNA expression of the gene I've knocked-down (from Hela cells) is lower than the mRNA expression of my control.
Gladly I saw that indeed the knock-down sample expresses lower FPKM values of that specific gene. great.
However, I notice very high values of some microRNA:
NR_106781 has a value of 1,460,000
NR_039666 has a value of 995,697
NR_039828 & NR_002574 & NR_037428 are around 15,000
and around 15 more tracks are above 4000
the command line I used:
cuffdiff -p 6 -b hg19/fasta/ -u --no-update-check -v -L control,condition -o /cuffdiff hg19refseq.gtf control/accepted_hits.bam condition/accepted_hits.bam
* I used Refseq hg19 downloaded from UCSC table browser
So these results obviously raises question:
Why those MicroRNA FPKM are so high ?
And how could FPKM values be over million considering that FPKM stands for fragments per kilo per million ?
Anyone ?
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