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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
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No alignment score in BAM file #56

Closed rahulk87 closed 4 years ago

rahulk87 commented 4 years ago

Hi,

I am running phaser and getting an error that there is no alignment score in the RNA-seq BAM file. I was wondering, if is there a way to run phaser without considering alignment score?

Many thanks, Rahul

secastel commented 4 years ago

Hi Rahul, Sorry for the delayed response. You can run phASER without alignment score by adding the argument "--as_q_cutoff 0". A word of caution, including AS will dramatically improve phasing quality from RNA-seq data. I'd suggest using using an RNA-seq alignment tool that includes alignment score.

Stephane

rahulk87 commented 4 years ago

Thanks Stephane, very helpful!!

On Sun, Nov 3, 2019 at 2:32 AM Stephane Castel notifications@github.com wrote:

Hi Rahul, Sorry for the delayed response. You can run phASER without alignment score by adding the argument "--as_q_cutoff 0". A word of caution, including AS will dramatically improve phasing quality from RNA-seq data. I'd suggest using using an RNA-seq alignment tool that includes alignment score.

Stephane

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