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dentearl / mafTools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
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mafCoverage output confusion, #5

Closed dentearl closed 10 years ago

dentearl commented 10 years ago

is the column labeled "lengthOfQueryGenome" really the query genome or the target genome?

Example output:

# targetSpecies/Chr querySpecies/Chr  lengthOfQueryGenome coverage
simHuman  simChimp  185145446 0.989333
simHuman  sHuman-sChimp 185145446 0.994176
simHuman  sG-sH-sC  185145446 0.992080
simHuman  simOrang  185145446 0.970797
simHuman  simHuman  185145446 0.012303
simHuman  simGorilla  185145446 0.985763
benedictpaten commented 10 years ago

Oops. So, I mixed up the first two field names - i.e. its supposed to be querySpecies targetSpecies lengthOfQueryGenome coverage, and everything else stays the same. I fixed the development branch.

On Thu, Jan 2, 2014 at 1:36 PM, Dent Earl notifications@github.com wrote:

is the column labeled "lengthOfQueryGenome" really the query genome or the target genome?

Example output:

targetSpecies/Chr querySpecies/Chr lengthOfQueryGenome coverage

simHuman simChimp 185145446 0.989333 simHuman sHuman-sChimp 185145446 0.994176 simHuman sG-sH-sC 185145446 0.992080 simHuman simOrang 185145446 0.970797 simHuman simHuman 185145446 0.012303 simHuman simGorilla 185145446 0.985763

— Reply to this email directly or view it on GitHubhttps://github.com/dentearl/mafTools/issues/5 .

benedictpaten commented 10 years ago

And now fixed on master too.

On Thu, Jan 2, 2014 at 2:05 PM, Benedict Paten benedict@soe.ucsc.eduwrote:

Oops. So, I mixed up the first two field names - i.e. its supposed to be querySpecies targetSpecies lengthOfQueryGenome coverage, and everything else stays the same. I fixed the development branch.

On Thu, Jan 2, 2014 at 1:36 PM, Dent Earl notifications@github.comwrote:

is the column labeled "lengthOfQueryGenome" really the query genome or the target genome?

Example output:

targetSpecies/Chr querySpecies/Chr lengthOfQueryGenome coverage

simHuman simChimp 185145446 0.989333 simHuman sHuman-sChimp 185145446 0.994176 simHuman sG-sH-sC 185145446 0.992080 simHuman simOrang 185145446 0.970797 simHuman simHuman 185145446 0.012303 simHuman simGorilla 185145446 0.985763

— Reply to this email directly or view it on GitHubhttps://github.com/dentearl/mafTools/issues/5 .

benedictpaten commented 10 years ago

Oops, I got query and reference the wrong way around, but now all fixed.

On Thu, Jan 2, 2014 at 2:18 PM, Benedict Paten benedict@soe.ucsc.eduwrote:

And now fixed on master too.

On Thu, Jan 2, 2014 at 2:05 PM, Benedict Paten benedict@soe.ucsc.eduwrote:

Oops. So, I mixed up the first two field names - i.e. its supposed to be querySpecies targetSpecies lengthOfQueryGenome coverage, and everything else stays the same. I fixed the development branch.

On Thu, Jan 2, 2014 at 1:36 PM, Dent Earl notifications@github.comwrote:

is the column labeled "lengthOfQueryGenome" really the query genome or the target genome?

Example output:

targetSpecies/Chr querySpecies/Chr lengthOfQueryGenome coverage

simHuman simChimp 185145446 0.989333 simHuman sHuman-sChimp 185145446 0.994176 simHuman sG-sH-sC 185145446 0.992080 simHuman simOrang 185145446 0.970797 simHuman simHuman 185145446 0.012303 simHuman simGorilla 185145446 0.985763

— Reply to this email directly or view it on GitHubhttps://github.com/dentearl/mafTools/issues/5 .