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Question: Differential gene expression results are different while using hg19 and hg38 genomic assembly
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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 |
ADD COMMENTlink 21 months ago akilabioinfo • 0 • updated 21 months ago Devon Ryan 90k
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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 COMMENTlink 21 months ago Devon Ryan 90k
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There's rarely a benefit to using stringTie in human data.

I did not knew that! Can you please elaborate?

ADD REPLYlink 21 months ago
Vijay Lakhujani
4.1k
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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 REPLYlink 21 months ago
Devon Ryan
90k
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Isn't StringTie a reference guided assembler and it provides both kinds of transcripts?

ADD REPLYlink 21 months ago
Vijay Lakhujani
4.1k
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Yes, but if you just want to quantify known transcripts then salmon or kallisto will do that MUCH faster.

ADD REPLYlink 21 months ago
Devon Ryan
90k
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There's rarely a benefit to using stringTie in human data. Is there is any reference for stringtie performance on human data?

ADD REPLYlink 21 months ago
akilabioinfo
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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 REPLYlink 21 months ago
Devon Ryan
90k

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