8000 phaser_gene_ae output with 0 Count? · Issue #65 · secastel/phaser · GitHub
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phaser_gene_ae output with 0 Count? #65

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deb0612 opened this issue Sep 7, 2020 · 1 comment
Open

phaser_gene_ae output with 0 Count? #65

deb0612 opened this issue Sep 7, 2020 · 1 comment

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@deb0612
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deb0612 commented Sep 7, 2020

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
@deb0612 deb0612 mentioned this issue Sep 10, 2020
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@secastel
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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.

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