Differential gene expression results are different while using hg19 and hg38 genomic assembly
1
0
Entering edit mode
3.5 years ago

Hi All,

I have aligned my fastq files using hg19 and hg38 genomic assembly using HISAT and i have performed differential gene expression analysis based on both the genomic assembly using cufflink, count and stringtie based protocol (table.1) . In this analysis i have obtained lesser number of differentially genes are common between both genomic assemblies. Have anybody face similar kind of results? Which method is reliable in this case? please help me

for example:

table.1 Number of differentially expressed genes obtained using hg19 and hg38 genomic assembly.

         | HG19 |  HG38 | common |
cufflink |  302 |   165 |     95 |
count    |   80 |    73 |     28 |
stringtie|  128 |   148 |     21 |
RNA-Seq galaxy cufflink featurecounts stringtie • 996 views
ADD COMMENT
1
Entering edit mode
3.5 years ago

You're likely observing a few different things. Firstly, hg19 has a number of problematic regions that cause aberrant alignments. These were largely fixed in hg38, which is one of the reasons people have transitioned to it. The other thing you're observing is that using different numbers and sizes of genes will result in different counts and thus different filtering and results from multiple testing adjustments.

For what it's worth, there is never a reason to use cufflinks any more. The authors don't even recommend using it. There's rarely a benefit to using stringTie in human data.

ADD COMMENT
0
Entering edit mode

There's rarely a benefit to using stringTie in human data.

I did not knew that! Can you please elaborate?

ADD REPLY
1
Entering edit mode

The point of stringTie is to assemble new transcripts that aren't annotated. There aren't many of those left for things like mouse and human.

ADD REPLY
0
Entering edit mode

Isn't StringTie a reference guided assembler and it provides both kinds of transcripts?

ADD REPLY
0
Entering edit mode

Yes, but if you just want to quantify known transcripts then salmon or kallisto will do that MUCH faster.

ADD REPLY
0
Entering edit mode

There's rarely a benefit to using stringTie in human data. Is there is any reference for stringtie performance on human data?

ADD REPLY
0
Entering edit mode

You can search pubmed for one of the numerous comparisons of differential expression programs. StringTie is useful when you have a poorly annotated organism or when you're interested in finding novel isoforms. Other than that there's never been a compelling reason to use it.

ADD REPLY

Login before adding your answer.

Traffic: 1813 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