Question: RNA-Seq High Expression Genes Lost
gravatar for madkisson
3.5 years ago by
United States
madkisson30 wrote:


I'm noticing that after running my BAM files through CuffDiff and CuffNorm that some genes that I know to be very highly expressed [Alb in liver should be 1M-2M reads; Gapdh should be fairly highly expressed] are showing zero [Alb] to under 20 reads [Gapdh]. I find the expected sized pile-ups when i check my BAM files on IGV. I'm certain this must be a parameter that can be adjusted in the Cuff* tools and is a consequence of many of these tools not really being written for full transcriptome RNA-Seq analysis. Any suggestions on how to fix this?

Here's my set up:
Mouse total RNA sequenced with Illumina HiSeq
Fastq to BAM files using TopHat2; defaults for all settings
BAM files straight to 'CuffDiff For CummeRbund' and 'CuffNorm' for tabular outputs; 3 Test replicates/5 Reference replicates
Using iGenome UCSC mm10 gtf file for both CuffDiff and CuffNorm


ADD COMMENTlink modified 2.5 years ago by ksriram0 • written 3.5 years ago by madkisson30
gravatar for ksriram
2.5 years ago by
ksriram0 wrote:

In Cufflinks, you will often get an error message saying 'HIDATA' and an FPKM value of 0. You need to increase the max number of fragments per locus; by default this is set to 10^6, you could increase this to say 10^7

ADD COMMENTlink written 2.5 years ago by ksriram0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour