Question: GATK ASEReadCounter: Downstream analysis for identifying allele specific expression
0
gravatar for komal.rathi
4 months ago by
komal.rathi3.0k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.0k wrote:

Hi everyone,

I am trying to find allele specific expression from RNA-seq data. I have the results from GATK ASEReadCounter and the output looks like this:

contig  position    variantID   refAllele   altAllele   refCount    altCount    totalCount  lowMAPQDepth    lowBaseQDepth   rawDepth    otherBases  improperPairs
chr2    38021   rs113895774 C   T   0   1   1   0   0   1   0   0
chr2    217334  rs6709534   G   C   0   3   3   0   0   3   0   0
chr2    218386  rs9213  G   A   84  101 185 0   0   185 0   0
chr2    220889  rs3828165   G   A   9   7   16  0   0   16  0   0
chr2    221560  rs60484953  G   A   11  11  22  0   0   22  0   0
chr2    221981  rs3791224   C   T   3   4   7   0   0   7   0   0
chr2    222336  rs3791223   T   C   3   8   11  0   0   11  0   0
chr2    224086  rs1474053   T   A   3   2   5   0   0   5   0   0
chr2    224919  rs2290911   A   G   55  16  71  0   0   71  0   0

I had an impression that this tool implements some test(s) to find statistically significant sites. But if I am not wrong, it only calculates the counts of ref and alt alleles based on RNA-seq - more or less like bam-readcount or samtools mpileup followed by counting bases.

In the manual of ASEReadCounter, they say that you can use the output format as input to mamba but I am not sure looking at the input format for mamba which requires an additional field: EXON_INFO - variant annotation label. Alternatively, I am thinking of using the refCount, altCount and totalCount, perform a chi square test to determine if there is allelic imbalance or not.

I would like to get suggestions on how to analyze this output or what downstream methods/statistical tests to use. Any help would be much appreciated.

Thanks!

ADD COMMENTlink modified 3 months ago by prasundutta87150 • written 4 months ago by komal.rathi3.0k
0
gravatar for prasundutta87
3 months ago by
prasundutta87150
prasundutta87150 wrote:

ASEReadCounter is doing what it says its doing..just counting the ref and alt reads per allele..

A chi square test or a two sided binomial test is fine for determining locus based ASE..for gene based there are other methods..you can get more information from this paper- http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=7297750

ADD COMMENTlink modified 3 months ago • written 3 months ago by prasundutta87150
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