Chris Boniface

My apologies - Sure, using the fgbio workflow as an example, say you have filtered your consensus calls by 2 reads required per family using FilterConsensusReads, you will have a...

Thanks for the suggestion - I'm still ruminating on it... I'll give it a test run on some data and let you know!

Sure - we've got a couple of papers but the data pipelines are old. The fgbio tools working much better ;) (publication links: https://pubmed.ncbi.nlm.nih.gov/33466369/, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861971/, https://pubmed.ncbi.nlm.nih.gov/30833418/) Basically the prep is...

1) there are multiple examples of this in a given library and the UMI involved don't seem to have any features in common (what I gave as an example was...

I have considered several mechanisms for these events and I'm thinking that since there isn't a significant amount of chimeras and the entire read typically maps fine, it is most...

I'm realizing that its not going to work as is (even if it wasn't prohibitively slow). I was doing a simple iteration through the position-sorted (filtered) consensus bam and comparing...

@tfenne Here are those reads pre and post ClipBam (these are uncompressed sams - wouldn't let me upload bams). Let me know if you need a different format. Thanks for...

Ahhh - thanks! I thought I had read through the tool description, I must have missed that. What's the thinking behind only clipping FR orientation, why not clip these RR...

I am having the same issue using version 0.2.0-0 - is there a fix for this? Thanks, Chris

Hi Gavin, I am having the same issue: Error in seqlevelsStyle(as.character(x)) : The style does not have a compatible entry for the species supported by Seqname. Please see genomeStyles() for...