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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
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phaser_gene_ae output with 0 Count? #65

Open deb0612 opened 4 years ago

deb0612 commented 4 years ago

When running "python ~/tools/phaser/phaser_gene_ae/phaser_gene_ae.py -- tast_case.haplotypic_counts.txt --features gencode.v19.GRCh37.genes.bed --o phaser_test_case_gene_ae.txt" command, the output file show 0 aCount, bCount and totalCount. Image 0240907 I checked the input haplotypic_counts file, and it show the Count number. Image 0250907

secastel commented 4 years ago

This is because the chromosome naming between the files going into phaser.py and the gene annotation file you are using for phaser_gene_ae.py. I can see that you don't have "chr" in the name of the contig for the gene annotation file, which doesn't match the outputs from phaser. Chromosome names must match or all counts will show up as 0, which is what you are seeing here.