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][1].

In the manual of ASEReadCounter, they say that you can use the output format as input to [mamba][2] 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!

  [1]: https://github.com/riverlee/pileup2base/blob/master/pileup2baseindel.pl
  [2]: http://www.well.ox.ac.uk/~rivas/mamba/
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

