Explore lite pipeline

[rcurrie]

Creating this ticket to evaluate a lighter weight pipeline using Kallisto for quantification.

[rcurrie]

@jpfeil @hbeale Pizzly is a fusion caller that goes with Kallisto

[rcurrie]

@hbeale mMaybe I was over thinking all the details. We essentially just need something that correlates with uniqMappedNonDupeReadCount. Once we have that we can scale appropriately. Preliminary attempt:

X = Total Reads * % Unique in first 100k of FASTQ Y = uniqMappedNonDupeReadCount

Will look into those flat liners with a bit more tooling. Make sense?

[hbeale]

The trend looks right.

We need a fraction so that we can apply it to the total number of exonic reads to get the number of non dupe exonic reads

On Fri, Jul 27, 2018 at 10:34 PM Rob Currie notifications@github.com wrote:

@hbeale https://github.com/hbeale mMaybe I was over thinking all the details. We essentially just need something that correlates with uniqMappedNonDupeReadCount. Once we have that we can scale appropriately. Preliminary attempt:

X = Total Reads * % Unique in first 100k of FASTQ Y = uniqMappedNonDupeReadCount

[image: image] https://user-images.githubusercontent.com/492570/43353396-b3c61120-91ec-11e8-9425-5e8eebb999ac.png

Will look into those flat liners with a bit more tooling. Make sense?

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[rcurrie]

Removing samples from the infamous THR33:

Proxy = # Total Pairs (from FASTQC) * % Pairs Unique in first 1M Pairs