PCA plot for miRNA
0
0
Entering edit mode
7 weeks ago
struggler • 0

Hi everyone,

I have RNAseq and sRNAseq data for one specific condition in plant. RNAseq data shows very well behaved pattern on PCA plot while miRNA does not show that pattern (not even biological sense) on PCA. Could anyone please help me to understand this issue?

miRNA PCA • 296 views
ADD COMMENT
0
Entering edit mode

What methods were used to quantify mRNA and miRNA from the raw fastq files ?

ADD REPLY
0
Entering edit mode

Hi Abhishek,

For miRNA, first I predicted novel miRNA by miRDP2 and then aligning clean reads over it to get count file. 1>made database for predicted novel miRNA 2> map all filtered read over it 3> sam file to count file by samtools.4> transformed by VST 5> plot PCA For mRNA, (other person is doing) he used feature count for mRNA quantification.

Hope I could clearly explain.

ADD REPLY
0
Entering edit mode

You might want to show examples of what the two PCA plots look like. PCA relies on the variation between your samples. Since RNA-seq has many more transcripts than your short RNA-seq, there are more instances of variation which would be more easily depicted on a PCA plot. This could potentially mean that your short RNA-seq data have little variation between conditions.

ADD REPLY
0
Entering edit mode

Hi Trivas,

Thanks for your answer. I have time series data from fresh(DT00) to dehydrated(DT03,06,09,12,15,24) to rehydrated condition(RT00,01,02,04,08,12,48) in one plant. My PCA plot shows dehydrated sample i.e DT24 comes closer to RT48 which should not be. Means both are completely opposite to each other while RNAseq PCA plot nicely distributed according to their water content. Here I am attaching PCA plot for miRNA while for mRNA can't as other person is doing. Hope I could make clear myself. enter image description here

ADD REPLY

Login before adding your answer.

Traffic: 1048 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6