Does the AI package also allow more than one seqlevel?
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@sannysandra93-9018
Last seen 5.9 years ago
Netherlands

Hi,

I am examining a sample on a MCF-7 cell line (of paired-end RNA seq data including the SNP array data) where I want to investigate the allelic imbalance Genome Wide, not just one specified region (for example: "searchArea"). This way, I could find genes where allelic imbalance occur instead of the other way around. I was wondering if the AllelicImbalance package allows more than one seqlevel for each BAM file. And what will be the alternative solution to this problem?

Kind regards,

Sandra

AllelicImbalance • 539 views
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lasfol ▴ 10
@lasfol-7894
Last seen 6.3 years ago
Technical University of Denmark
Hi! We are working on it - see the github discussion https://github.com/pappewaio/AllelicImbalance/issues/6 Welcome to join that and come with a request for multi-seqlevels. That specific part should actually be quite fixable. /Lasse > sannysandra93 posted the Question: "Does the AI package also allow more > than one seqlevel?": > > Hi, I am examining a sample on a MCF-7 cell line (of paired-end RNA seq > data including the SNP array data) where I want to investigate the allelic > imbalance Genome Wide, not just one specified region (for example: > "searchArea"). This way, I could find genes where allelic imbalance occur > instead of the other way around. I was wondering if the AllelicImbalance > package allows more than one seqlevel for each BAM file. And what will be > the alternative solution to this problem? Kind regards, Sandra > > --- > See the full post at: Does the AI package also allow more than one seqlevel? > Replying to this email will post an answer to the question above. >
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