Hi All, I would like to analyze the allele-specific expression in one sample at a specific het site (using rna seq data). I am not sure which of these two equations is correct. Could you please help me
- Equation one:
alt reads/total reads - Equation two:
| 0.5 - alt reads/total reads |
I found equation two in several papers but I don’t know what the 0.5 means
Thank you very much
1 answer
Thats the deviation from the expected 0.5.
If you have 100 reads overlapping a het SNP, if 25 coming from ref and 75 coming from alt, Allelic Ratio (AR) w.r.t ref allele is ref/total
25/100 = 0.25 . So the deviation is 0.5-0.25=0.25
If there is no allelic imbalance, the ref reads would be 50 and alternate reads would be 50, AR is 0.5 and deviation would be 0.5-0.5=0, i.e no allelic imbalance.
I would just do ref/total to have AR. No need to do (0.5-ref/total). You need to do a binomial test to see the "significant" deviation.
PS: It doesnt matter if numerator is ref or alt count. When you interpret, it should be w.r.t what you use as numerator. Like in gene expression fold change, depending on if you compare condition1 vs condition2 or condition2 vs condition1
Log in to answer this question.
-
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
written by Fernando •
-
Filter on Allele Balance using BCFTools
written by sumudu_rangika •
-
What number I should specify for SMARTer Stranded Total RNA-Seq Kit v2 for --forward-prob in RSEM?
written by John
-
Normalization of allele specific counts in RNA-seq
written by Ankit
-
allele specific expression (ASE) reference ratio plot query
written by prasundutta87
-
Allele Specific Expression Analysis
written by Susmita Mandal
-
How to get counts data for allele specific expression analysis (ASE) from aligned bam files (RNA-se…
written by Naresh D J •
-
HTseq or featureCounts without gff file
written by arta
-
WGCNA requires always a trait data?
written by adriana.gallego.02 •
-
In TCGA RNA-seq exon specific data, why not all the exons of a particular isoform have similar read…
written by ruhulmb •
Thank you very much for your response @geek_y :)
The problem now is that my BAM file shows the the ref and alt reads but this site is completely absent in the VCF :/..Any ideas how I can resolve that? or can I just determine the number of ref and alt reads from the BAM file?
Please use
ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized. This comment show go under @geek_y's answer.SUBMIT ANSWERis for new answers to original question.How did you get that VCF file ? Genotyping array ?
no targeted sequencing