David Eccles (gringer)

Inconsistent read counts with transcript isoforms ending at different locations (unsupported by reads)

5

We've found another odd result in our transcript count data surrounding the gene Apex1 (and at least one other similar gene). This gene has three transcript isoforms that were counted...

Inconsistent read counts within polycistronic transcripts with near-constant expression

2

In our mouse cDNA data, we hypothesise that mt-Atp6 and mt-Atp8 are encoded together on the mouse mitochondrial genome as a single polycistronic unit, which is demonstrated by observing co-expression...

Extreme mismatch between JBrowse coverage and Bambu mapping (moderate vs 0 expression)

4

After reporting Bambu results to the biologists I have been working with, they noticed a number of odd counting behaviours from the Bambu output. One gene in particular that surprised...

alevinQC doesn't seem to work with salmon v1.9.0

1

I've recently mapped some reads that I'd like to create a summary report for, but alevinQC doesn't seem to recognise the format: ``` > alevinQCReport(baseDir = baseDir, sampleId = "testSample",...

3D Honeycomb - switch direction at smallest bridge point, rather than every layer

8

This is an update to the 3D Honeycomb / Truncated Octahedron infill to make the infill pattern a lot stronger, and more likely to hold at very low infill percentages....

I've been previously processing my data using Salmon Alevin. We've just got our results back from a SevenBridges analysis of our single cell sequencing data, and there's a substantial difference...

Integer overflow in metadata info file

2

Using salmon alevin v1.9.0, I noticed that my *total* reads were less than the deduplicated UMI count when I combined all three libraries together (from a NovaSeq run): ``` {...

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?** Both, but salmon / bulk mode in this instance **Describe the bug** Salmon appears to have a...

**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?** Salmon (bulk mode) **Describe the bug** For one of our 41 samples, salmon fails (quits, without any...

With the new PCB111 and PCB114 kits, ONT are using a new strand-switch primer that incorporates a UMI tag. I've now worked out how I can slot that UMI information...