NA is coming up as a gene name

[cnobles]

No description provided.

[anatolydryga]

@cnobles for what dataset(patient) and where in the report?

[cnobles]

If you want to test, check patient "p04409-10". NA appears in the barcharts, sharing heatmap, and wordclouds.

[anatolydryga]

indeed it is, I will work on it.

[anatolydryga]

we have reads mapped to chrM
very often to position 12460

but refSeq gene tables does not have chrM

so when getNearestFeature is called for
sites with chrM NA is produced

solutions:
filter chrM
???

[cnobles]

SELECT DISTINCT samples.miseqid FROM samples INNER JOIN sites ON samples.sampleID = sites.sampleID WHERE chr = "chrM"

All the runs containing sites which match to chrM sites.

[cnobles]

SELECT DISTINCT samples.miseqid, COUNT(miseqid) AS chrM_Hits FROM samples INNER JOIN sites ON samples.sampleID = sites.sampleID WHERE chr = "chrM" GROUP BY miseqid

How many chrM hits per run. We should focus on grabbing the reads from the February runs.

[chasberry]

Is it biologically possible to have integration events in the mitochondria?

If not where do these "sites" come from?

If so, NA or Inf seem like plausible choices for constructing a dataset with filtering done downstream.

[cnobles]

There currently isn't much support for mitochondrial integration, if any. I'm currently looking into where these reads are coming from and what there origins may be. I'll be able to update everyone soon on their legitimacy, or if they are contaminants / artifacts.

[cnobles]

Update: Data suggests a large part of the problem is the LTRbit filtering is too permissive. We looked back in the intSiteLogic.R code and found which line should be changed. We are currently adjusting the parameters to be more stringent and rerunning some of the runs to check performance.

[cnobles]

Another part of the problem is reads that map to chrM but also map (at slightly lower quality) to chr#. This can occur as the DNA of mitochondria has been slowly assimilated into the eukaryotic genome over time, and therefore there are regions of the human genome which highly resemble regions of the mitochondrial genome.