User: monaallouba

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Posts by monaallouba

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Comment: C: Allele specific expression
... no targeted sequencing ...
written 7 days ago by monaallouba0
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ref and alt allele count from BAM file
... Hi All, I would like to calculate the allele ratio of ref/alt at a specific position. How can I determine the ref and alt counts from the BAM file? (or is it better to extract this info from the VCF?) Thank you ...
bam allele_count rna-seq written 24 days ago by monaallouba0 • updated 24 days ago by Vitis2.2k
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Comment: A: Allele specific expression
... Thank you very much for your response @geek_y :) The problem now is that my BAM file shows the the ref and alt reads but this site is completely absent in the VCF :/..Any ideas how I can resolve that? or can I just determine the number of ref and alt reads from the BAM file? ...
written 24 days ago by monaallouba0
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Comment: C: Allele Specific Expression Analysis
... does ASEReadCounter work for INDELs? as I tried using it and did not get any results ...
written 25 days ago by monaallouba0
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Allele specific expression
... Hi All, I would like to analyze the allele-specific expression in one sample at a specific het site (using rna seq data). I am not sure which of these two equations is correct. Could you please help me 1. Equation one: `alt reads/total reads` 2. Equation two: `| 0.5 - alt reads/total reads |` I fo ...
allele-specific expression rna-seq written 25 days ago by monaallouba0

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