checking allelic expression from SNP showing both Biallelic and monoallelic expression for sample gene
0
0
Entering edit mode
8 weeks ago

Hello folks,

I am trying see the allelic expression from RNA seq data for that I have used heterozygous SNPs from VCF file, using GATK asereadcounter got the SNPs count problem I am confused with a genes SNPs showing both biallelic count and monoallelic count any one suggest what will be the issue below giving some examples

     ID          Chromosome SNP Ref Alt gene_name
ENSMUSG00000033845  1   4774188 12  0   Mrpl15
ENSMUSG00000033845  1   4774538 10  0   Mrpl15
ENSMUSG00000033845  1   4775069 10  0   Mrpl15
ENSMUSG00000033845  1   4775803 10  0   Mrpl15
ENSMUSG00000033845  1   4776734 300 203 Mrpl15
ENSMUSG00000033845  1   4781549 2   8   Mrpl15
ENSMUSG00000033845  1   4782730 365 241 Mrpl15
ENSMUSG00000033845  1   4785703 122 136 Mrpl15
ENSMUSG00000033813  1   4857943 387 370 Tcea1
ENSMUSG00000033813  1   4896452 37  5   Tcea1
ENSMUSG00000033813  1   4896518 78  5   Tcea1
ENSMUSG00000033813  1   4897736 18  0   Tcea1
ENSMUSG00000033813  1   4897745 16  0   Tcea1
ENSMUSG00000033793  1   5095686 0   373 Atp6v1h
ENSMUSG00000033793  1   5124338 0   395 Atp6v1h
ENSMUSG00000033793  1   5162288 50  69  Atp6v1h
ENSMUSG00000033793  1   5162341 34  45  Atp6v1h
ENSMUSG00000033793  1   5162347 26  42  Atp6v1h
ENSMUSG00000046101  1   9941079 0   10  6030422M02Rik
ENSMUSG00000046101  1   9942048 9   13  6030422M02Rik
ENSMUSG00000036850  2   24974162    51  101 Mrpl41
ENSMUSG00000036850  2   24974614    0   482 Mrpl41
ENSMUSG00000036850  2   24974997    7   301 Mrpl41
ENSMUSG00000003131  9   45965680    0   88  Pafah1b2
ENSMUSG00000003131  9   45965880    0   163 Pafah1b2
ENSMUSG00000003131  9   45966221    93  48  Pafah1b2
ENSMUSG00000003131  9   45966516    108 106 Pafah1b2
ENSMUSG00000003131  9   45966539    139 101 Pafah1b2
ENSMUSG00000003131  9   45966968    0   332 Pafah1b2
ENSMUSG00000003131  9   45967403    0   240 Pafah1b2
ENSMUSG00000003131  9   45967446    0   296 Pafah1b2
ENSMUSG00000003131  9   45967547    3   207 Pafah1b2
ENSMUSG00000003131  9   45967758    0   36  Pafah1b2

Thank you

Single-Cell-RNA-seq SNP RNA-Seq ASEreadcounter allelic • 161 views
ADD COMMENT

Login before adding your answer.

Traffic: 2209 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